Starting phenix.real_space_refine on Wed Mar 4 13:58:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgr_31977/03_2026/7vgr_31977.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgr_31977/03_2026/7vgr_31977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vgr_31977/03_2026/7vgr_31977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgr_31977/03_2026/7vgr_31977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vgr_31977/03_2026/7vgr_31977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgr_31977/03_2026/7vgr_31977.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5356 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6320 2.51 5 N 1642 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9872 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1687 Chain: "D" Number of atoms: 1639 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1627 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 220, 1627 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 1656 Chain: "E" Number of atoms: 1693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1687 Chain: "F" Number of atoms: 1639 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1627 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 220, 1627 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 1656 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1604 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "B" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1604 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Time building chain proxies: 3.45, per 1000 atoms: 0.35 Number of scatterers: 9872 At special positions: 0 Unit cell: (95.865, 140.685, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1860 8.00 N 1642 7.00 C 6320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS D 147 " - pdb=" SG ACYS D 202 " distance=2.03 Simple disulfide: pdb=" SG BCYS D 147 " - pdb=" SG BCYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS F 147 " - pdb=" SG ACYS F 202 " distance=2.03 Simple disulfide: pdb=" SG BCYS F 147 " - pdb=" SG BCYS F 202 " distance=2.03 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: 0.78 Conformation dependent library (CDL) restraints added in 705.7 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 22 sheets defined 19.2% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.179A pdb=" N VAL C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.639A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 83 through 87 removed outlier: 4.179A pdb=" N VAL E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.639A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'A' and resid 10 through 37 Processing helix chain 'A' and resid 43 through 71 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 76 through 106 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.734A pdb=" N SER A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 112 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 37 Processing helix chain 'B' and resid 43 through 71 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 76 through 106 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.734A pdb=" N SER B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 112 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.625A pdb=" N PHE C 75 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.426A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 122 removed outlier: 6.204A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.893A pdb=" N ASN C 149 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 201 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS C 153 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 197 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.505A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.598A pdb=" N GLU D 10 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 131 removed outlier: 3.749A pdb=" N VAL D 143 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER D 185 " --> pdb=" O PRO D 174 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER D 187 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR D 172 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR D 189 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL D 170 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.649A pdb=" N HIS D 206 " --> pdb=" O THR D 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.626A pdb=" N PHE E 75 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.427A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET E 37 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR E 53 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 122 removed outlier: 6.203A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.893A pdb=" N ASN E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR E 201 " --> pdb=" O ASN E 149 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS E 153 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR E 197 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N HIS E 202 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER E 207 " --> pdb=" O HIS E 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.505A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.598A pdb=" N GLU F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 49 through 51 Processing sheet with id=AB8, first strand: chain 'F' and resid 127 through 131 removed outlier: 3.748A pdb=" N VAL F 143 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR F 182 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER F 185 " --> pdb=" O PRO F 174 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER F 187 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR F 172 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR F 189 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL F 170 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.650A pdb=" N HIS F 206 " --> pdb=" O THR F 211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 128 through 133 removed outlier: 4.004A pdb=" N ILE A 118 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 121 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE A 168 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 200 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS A 180 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG A 198 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY A 182 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR A 196 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.672A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 128 through 133 removed outlier: 4.003A pdb=" N ILE B 118 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN B 121 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE B 168 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 200 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS B 180 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG B 198 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY B 182 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR B 196 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.671A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3097 1.34 - 1.46: 2528 1.46 - 1.58: 4439 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 10134 Sorted by residual: bond pdb=" CA LEU A 164 " pdb=" CB LEU A 164 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.83e-02 2.99e+03 1.60e+00 bond pdb=" CA LEU B 164 " pdb=" CB LEU B 164 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.83e-02 2.99e+03 1.57e+00 bond pdb=" N ARG A 174 " pdb=" CA ARG A 174 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 bond pdb=" N ARG B 174 " pdb=" CA ARG B 174 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.97e-01 bond pdb=" CG PRO A 165 " pdb=" CD PRO A 165 " ideal model delta sigma weight residual 1.503 1.536 -0.033 3.40e-02 8.65e+02 9.64e-01 ... (remaining 10129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 13675 2.17 - 4.33: 129 4.33 - 6.50: 22 6.50 - 8.67: 2 8.67 - 10.83: 2 Bond angle restraints: 13830 Sorted by residual: angle pdb=" C ILE A 161 " pdb=" N LYS A 162 " pdb=" CA LYS A 162 " ideal model delta sigma weight residual 121.54 132.37 -10.83 1.91e+00 2.74e-01 3.22e+01 angle pdb=" C ILE B 161 " pdb=" N LYS B 162 " pdb=" CA LYS B 162 " ideal model delta sigma weight residual 121.54 132.36 -10.82 1.91e+00 2.74e-01 3.21e+01 angle pdb=" N ILE A 201 " pdb=" CA ILE A 201 " pdb=" C ILE A 201 " ideal model delta sigma weight residual 111.88 107.38 4.50 1.06e+00 8.90e-01 1.80e+01 angle pdb=" N ILE B 201 " pdb=" CA ILE B 201 " pdb=" C ILE B 201 " ideal model delta sigma weight residual 111.88 107.39 4.49 1.06e+00 8.90e-01 1.80e+01 angle pdb=" N LYS A 162 " pdb=" CA LYS A 162 " pdb=" CB LYS A 162 " ideal model delta sigma weight residual 110.49 115.32 -4.83 1.69e+00 3.50e-01 8.16e+00 ... (remaining 13825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 5690 16.91 - 33.83: 268 33.83 - 50.74: 41 50.74 - 67.66: 7 67.66 - 84.57: 12 Dihedral angle restraints: 6018 sinusoidal: 2278 harmonic: 3740 Sorted by residual: dihedral pdb=" CB ACYS F 147 " pdb=" SG ACYS F 147 " pdb=" SG ACYS F 202 " pdb=" CB ACYS F 202 " ideal model delta sinusoidal sigma weight residual 93.00 58.62 34.38 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CB ACYS D 147 " pdb=" SG ACYS D 147 " pdb=" SG ACYS D 202 " pdb=" CB ACYS D 202 " ideal model delta sinusoidal sigma weight residual 93.00 58.85 34.15 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" CA SER E 71 " pdb=" C SER E 71 " pdb=" N ARG E 72 " pdb=" CA ARG E 72 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 923 0.027 - 0.054: 395 0.054 - 0.081: 137 0.081 - 0.108: 88 0.108 - 0.135: 27 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CA ILE E 79 " pdb=" N ILE E 79 " pdb=" C ILE E 79 " pdb=" CB ILE E 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE B 201 " pdb=" N ILE B 201 " pdb=" C ILE B 201 " pdb=" CB ILE B 201 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1567 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO D 156 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 155 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO F 156 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO F 156 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 156 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 96 " -0.013 2.00e-02 2.50e+03 1.11e-02 2.16e+00 pdb=" CG PHE A 96 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 96 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 96 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 96 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 96 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 96 " -0.003 2.00e-02 2.50e+03 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2013 2.79 - 3.32: 8910 3.32 - 3.84: 16400 3.84 - 4.37: 18662 4.37 - 4.90: 32954 Nonbonded interactions: 78939 Sorted by model distance: nonbonded pdb=" O VAL A 139 " pdb=" NH1 ARG B 150 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG A 150 " pdb=" O VAL B 139 " model vdw 2.295 3.120 nonbonded pdb=" NH1 ARG C 24 " pdb=" OD1 ASP C 74 " model vdw 2.302 3.120 nonbonded pdb=" NH1 ARG E 24 " pdb=" OD1 ASP E 74 " model vdw 2.302 3.120 nonbonded pdb=" OG SER E 166 " pdb=" O PRO F 174 " model vdw 2.309 3.040 ... (remaining 78934 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.27 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.410 Find NCS groups from input model: 0.070 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.002 0.043 10144 Z= 0.104 Angle : 0.554 10.835 13850 Z= 0.297 Chirality : 0.040 0.135 1570 Planarity : 0.004 0.038 1742 Dihedral : 10.586 84.569 3600 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.63 % Favored : 94.21 % Rotamer: Outliers : 0.18 % Allowed : 0.37 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.41 (0.24), residues: 1274 helix: 1.41 (0.36), residues: 206 sheet: -0.07 (0.23), residues: 524 loop : -1.08 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 220 TYR 0.007 0.001 TYR B 95 PHE 0.025 0.001 PHE A 96 TRP 0.020 0.001 TRP B 58 HIS 0.002 0.000 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00215 (10134) covalent geometry : angle 0.55434 (13830) SS BOND : bond 0.00143 ( 10) SS BOND : angle 0.61125 ( 20) hydrogen bonds : bond 0.21788 ( 410) hydrogen bonds : angle 7.74452 ( 1076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.413 Fit side-chains REVERT: C 36 PHE cc_start: 0.7922 (m-10) cc_final: 0.7694 (m-80) REVERT: C 46 GLN cc_start: 0.8048 (mt0) cc_final: 0.7806 (mt0) REVERT: C 85 ASP cc_start: 0.8004 (t0) cc_final: 0.7696 (OUTLIER) REVERT: C 107 LYS cc_start: 0.8359 (tttt) cc_final: 0.7851 (ttpt) REVERT: C 119 VAL cc_start: 0.8262 (t) cc_final: 0.7887 (t) REVERT: D 20 ILE cc_start: 0.8791 (mt) cc_final: 0.8280 (mp) REVERT: D 46 GLU cc_start: 0.7386 (tt0) cc_final: 0.7047 (mt-10) REVERT: D 211 THR cc_start: 0.7861 (m) cc_final: 0.7511 (p) REVERT: E 12 THR cc_start: 0.8973 (t) cc_final: 0.8717 (m) REVERT: E 107 LYS cc_start: 0.8339 (tttt) cc_final: 0.7993 (ttpt) REVERT: E 119 VAL cc_start: 0.8659 (t) cc_final: 0.8400 (t) REVERT: E 194 ASN cc_start: 0.7207 (t0) cc_final: 0.6960 (t0) REVERT: F 20 ILE cc_start: 0.8829 (mt) cc_final: 0.8223 (mp) REVERT: F 150 LYS cc_start: 0.8208 (tttm) cc_final: 0.7969 (ttpp) REVERT: F 211 THR cc_start: 0.8111 (m) cc_final: 0.7779 (p) REVERT: B 127 THR cc_start: 0.8055 (p) cc_final: 0.7783 (t) outliers start: 0 outliers final: 1 residues processed: 282 average time/residue: 0.5621 time to fit residues: 169.6953 Evaluate side-chains 185 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 170 GLN D 6 GLN D 39 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN F 6 GLN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN B 113 ASN B 148 HIS B 155 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094590 restraints weight = 38414.472| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.29 r_work: 0.3034 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10144 Z= 0.269 Angle : 0.775 9.186 13850 Z= 0.394 Chirality : 0.050 0.224 1570 Planarity : 0.005 0.035 1742 Dihedral : 4.831 20.437 1406 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.69 % Allowed : 10.98 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.44 (0.24), residues: 1274 helix: 0.58 (0.35), residues: 212 sheet: 0.11 (0.23), residues: 530 loop : -0.99 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 40 TYR 0.023 0.003 TYR F 129 PHE 0.018 0.003 PHE A 26 TRP 0.034 0.003 TRP A 58 HIS 0.006 0.002 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00648 (10134) covalent geometry : angle 0.77403 (13830) SS BOND : bond 0.00513 ( 10) SS BOND : angle 1.33769 ( 20) hydrogen bonds : bond 0.04891 ( 410) hydrogen bonds : angle 5.67424 ( 1076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.315 Fit side-chains REVERT: C 107 LYS cc_start: 0.8786 (tttt) cc_final: 0.7860 (ttpt) REVERT: C 128 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7642 (tm-30) REVERT: C 167 TRP cc_start: 0.8916 (m-90) cc_final: 0.8698 (m-90) REVERT: C 214 ASN cc_start: 0.7256 (m-40) cc_final: 0.6940 (m-40) REVERT: D 73 ASP cc_start: 0.7918 (t0) cc_final: 0.7653 (t0) REVERT: D 211 THR cc_start: 0.7287 (m) cc_final: 0.7039 (m) REVERT: D 216 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8036 (ttpp) REVERT: E 12 THR cc_start: 0.9126 (t) cc_final: 0.8634 (m) REVERT: E 72 ARG cc_start: 0.7438 (ttp-110) cc_final: 0.6892 (ptm-80) REVERT: E 107 LYS cc_start: 0.8758 (tttt) cc_final: 0.7828 (ttpt) REVERT: E 128 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: E 141 ASN cc_start: 0.8163 (m110) cc_final: 0.7917 (m110) REVERT: E 167 TRP cc_start: 0.8926 (m-90) cc_final: 0.8704 (m-90) REVERT: F 20 ILE cc_start: 0.8799 (mt) cc_final: 0.8514 (mt) REVERT: F 40 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7920 (mmm160) REVERT: F 74 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7175 (mtmm) REVERT: F 150 LYS cc_start: 0.7815 (tttm) cc_final: 0.7487 (ttpp) REVERT: F 211 THR cc_start: 0.7407 (m) cc_final: 0.7139 (m) REVERT: A 205 LYS cc_start: 0.6561 (mttt) cc_final: 0.6263 (mttt) outliers start: 38 outliers final: 14 residues processed: 217 average time/residue: 0.5711 time to fit residues: 132.3716 Evaluate side-chains 174 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 164 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 214 ASN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.091517 restraints weight = 46939.860| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.60 r_work: 0.2966 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10144 Z= 0.215 Angle : 0.675 8.562 13850 Z= 0.346 Chirality : 0.046 0.180 1570 Planarity : 0.004 0.031 1742 Dihedral : 4.820 22.026 1406 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.78 % Allowed : 13.19 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 (0.24), residues: 1274 helix: 0.66 (0.35), residues: 212 sheet: 0.23 (0.23), residues: 530 loop : -0.93 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 159 TYR 0.017 0.002 TYR E 196 PHE 0.014 0.002 PHE F 109 TRP 0.020 0.002 TRP B 58 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00522 (10134) covalent geometry : angle 0.67393 (13830) SS BOND : bond 0.00379 ( 10) SS BOND : angle 1.12893 ( 20) hydrogen bonds : bond 0.04160 ( 410) hydrogen bonds : angle 5.34366 ( 1076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.301 Fit side-chains REVERT: C 27 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: C 72 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.6687 (ptm-80) REVERT: C 83 GLU cc_start: 0.8132 (mp0) cc_final: 0.7597 (pm20) REVERT: C 107 LYS cc_start: 0.8803 (tttt) cc_final: 0.8483 (mtpm) REVERT: C 128 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7887 (tm-30) REVERT: C 214 ASN cc_start: 0.7154 (m-40) cc_final: 0.6899 (m-40) REVERT: D 20 ILE cc_start: 0.8688 (mt) cc_final: 0.8328 (mp) REVERT: D 73 ASP cc_start: 0.8020 (t0) cc_final: 0.7648 (t0) REVERT: D 211 THR cc_start: 0.7341 (m) cc_final: 0.7059 (m) REVERT: D 216 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7986 (ttpp) REVERT: E 12 THR cc_start: 0.9097 (t) cc_final: 0.8644 (m) REVERT: E 18 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7805 (ptp90) REVERT: E 27 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8205 (pm20) REVERT: E 37 MET cc_start: 0.8829 (tpp) cc_final: 0.8570 (tpp) REVERT: E 72 ARG cc_start: 0.7341 (ttp-110) cc_final: 0.6643 (ptm-80) REVERT: E 83 GLU cc_start: 0.8385 (mp0) cc_final: 0.8116 (mt-10) REVERT: E 107 LYS cc_start: 0.8830 (tttt) cc_final: 0.7865 (tptt) REVERT: E 167 TRP cc_start: 0.8921 (m-90) cc_final: 0.8717 (m-90) REVERT: F 20 ILE cc_start: 0.8834 (mt) cc_final: 0.8350 (mp) REVERT: F 74 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7230 (mtmm) REVERT: F 150 LYS cc_start: 0.7928 (tttm) cc_final: 0.7557 (ttpp) REVERT: F 211 THR cc_start: 0.7499 (m) cc_final: 0.7212 (m) REVERT: A 205 LYS cc_start: 0.6670 (mttt) cc_final: 0.6241 (mttt) REVERT: B 74 ASN cc_start: 0.7483 (p0) cc_final: 0.7248 (p0) REVERT: B 190 ASP cc_start: 0.7586 (m-30) cc_final: 0.7314 (t0) outliers start: 37 outliers final: 16 residues processed: 186 average time/residue: 0.6397 time to fit residues: 126.7216 Evaluate side-chains 180 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 77 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS B 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.141458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088538 restraints weight = 38671.753| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.42 r_work: 0.2936 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10144 Z= 0.243 Angle : 0.706 8.520 13850 Z= 0.360 Chirality : 0.047 0.174 1570 Planarity : 0.004 0.030 1742 Dihedral : 4.984 22.776 1406 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.87 % Allowed : 13.84 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.32 (0.24), residues: 1274 helix: 0.54 (0.34), residues: 212 sheet: 0.25 (0.23), residues: 530 loop : -0.92 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 112 TYR 0.013 0.002 TYR E 196 PHE 0.012 0.002 PHE D 109 TRP 0.015 0.002 TRP D 47 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00591 (10134) covalent geometry : angle 0.70526 (13830) SS BOND : bond 0.00417 ( 10) SS BOND : angle 1.24085 ( 20) hydrogen bonds : bond 0.04195 ( 410) hydrogen bonds : angle 5.30399 ( 1076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.361 Fit side-chains REVERT: C 27 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: C 72 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6831 (ptm-80) REVERT: C 83 GLU cc_start: 0.8344 (mp0) cc_final: 0.8104 (mt-10) REVERT: C 107 LYS cc_start: 0.8681 (tttt) cc_final: 0.8343 (mtpm) REVERT: C 128 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7887 (tm-30) REVERT: C 199 GLU cc_start: 0.8152 (tt0) cc_final: 0.7782 (tt0) REVERT: D 20 ILE cc_start: 0.8662 (mt) cc_final: 0.8285 (mp) REVERT: D 59 ASN cc_start: 0.8398 (m110) cc_final: 0.8169 (m110) REVERT: D 73 ASP cc_start: 0.8017 (t0) cc_final: 0.7515 (t0) REVERT: D 74 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7363 (mtmm) REVERT: D 211 THR cc_start: 0.7125 (m) cc_final: 0.6852 (m) REVERT: E 12 THR cc_start: 0.9105 (t) cc_final: 0.8660 (m) REVERT: E 18 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7801 (ptp90) REVERT: E 27 GLU cc_start: 0.8596 (pt0) cc_final: 0.8227 (pm20) REVERT: E 59 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: E 72 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.6801 (ptm-80) REVERT: E 83 GLU cc_start: 0.8224 (mp0) cc_final: 0.7992 (mt-10) REVERT: E 107 LYS cc_start: 0.8710 (tttt) cc_final: 0.7727 (tptt) REVERT: E 128 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7570 (tm-30) REVERT: E 174 ASP cc_start: 0.8351 (p0) cc_final: 0.8135 (p0) REVERT: F 20 ILE cc_start: 0.8809 (mt) cc_final: 0.8514 (mt) REVERT: F 74 LYS cc_start: 0.7598 (mtpt) cc_final: 0.7117 (mtmm) REVERT: F 150 LYS cc_start: 0.7868 (tttm) cc_final: 0.7495 (ttpp) REVERT: F 211 THR cc_start: 0.7358 (m) cc_final: 0.7058 (m) REVERT: A 190 ASP cc_start: 0.7618 (m-30) cc_final: 0.7391 (t0) REVERT: A 205 LYS cc_start: 0.6698 (mttt) cc_final: 0.6271 (mttt) REVERT: B 190 ASP cc_start: 0.7603 (m-30) cc_final: 0.7345 (t0) outliers start: 38 outliers final: 22 residues processed: 180 average time/residue: 0.6213 time to fit residues: 119.2306 Evaluate side-chains 171 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 40 optimal weight: 0.0000 chunk 100 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.145264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.092591 restraints weight = 52985.065| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.87 r_work: 0.2997 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10144 Z= 0.123 Angle : 0.608 8.168 13850 Z= 0.309 Chirality : 0.043 0.132 1570 Planarity : 0.004 0.033 1742 Dihedral : 4.552 22.322 1406 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.32 % Allowed : 14.85 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.07 (0.24), residues: 1274 helix: 0.91 (0.35), residues: 212 sheet: 0.42 (0.23), residues: 528 loop : -0.85 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 40 TYR 0.012 0.001 TYR E 196 PHE 0.015 0.001 PHE E 32 TRP 0.010 0.001 TRP C 167 HIS 0.002 0.000 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00292 (10134) covalent geometry : angle 0.60815 (13830) SS BOND : bond 0.00195 ( 10) SS BOND : angle 0.71449 ( 20) hydrogen bonds : bond 0.03386 ( 410) hydrogen bonds : angle 4.94365 ( 1076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: C 27 GLU cc_start: 0.8633 (pt0) cc_final: 0.8272 (pm20) REVERT: C 72 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6749 (ptm-80) REVERT: C 83 GLU cc_start: 0.8178 (mp0) cc_final: 0.7867 (mt-10) REVERT: C 107 LYS cc_start: 0.8770 (tttt) cc_final: 0.8440 (mtpm) REVERT: C 128 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7850 (tm-30) REVERT: D 20 ILE cc_start: 0.8658 (mt) cc_final: 0.8304 (mp) REVERT: D 73 ASP cc_start: 0.8029 (t0) cc_final: 0.7463 (m-30) REVERT: D 74 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7498 (mtmm) REVERT: D 211 THR cc_start: 0.7092 (m) cc_final: 0.6805 (m) REVERT: E 12 THR cc_start: 0.9122 (t) cc_final: 0.8673 (m) REVERT: E 18 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7823 (ptp90) REVERT: E 72 ARG cc_start: 0.7561 (ttp-110) cc_final: 0.6846 (ptm-80) REVERT: E 83 GLU cc_start: 0.8023 (mp0) cc_final: 0.7817 (mt-10) REVERT: E 107 LYS cc_start: 0.8721 (tttt) cc_final: 0.7752 (tptt) REVERT: E 128 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7514 (tm-30) REVERT: E 159 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8432 (mmm-85) REVERT: F 20 ILE cc_start: 0.8810 (mt) cc_final: 0.8311 (mp) REVERT: F 74 LYS cc_start: 0.7500 (mtpt) cc_final: 0.7080 (mtmm) REVERT: F 103 GLU cc_start: 0.8881 (pm20) cc_final: 0.8560 (pm20) REVERT: F 150 LYS cc_start: 0.7909 (tttm) cc_final: 0.7506 (ttpp) REVERT: F 211 THR cc_start: 0.7340 (m) cc_final: 0.7039 (m) REVERT: F 215 LYS cc_start: 0.6902 (tppp) cc_final: 0.6136 (tppt) REVERT: A 64 CYS cc_start: 0.7592 (t) cc_final: 0.7223 (m) REVERT: A 128 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8648 (mm) REVERT: A 190 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7177 (t0) REVERT: A 205 LYS cc_start: 0.6682 (mttt) cc_final: 0.6263 (mttt) REVERT: B 64 CYS cc_start: 0.7521 (t) cc_final: 0.7151 (m) REVERT: B 201 ILE cc_start: 0.9224 (tt) cc_final: 0.9022 (tp) outliers start: 32 outliers final: 16 residues processed: 181 average time/residue: 0.6704 time to fit residues: 128.7171 Evaluate side-chains 174 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.140648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.088470 restraints weight = 41841.250| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.46 r_work: 0.2930 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 10144 Z= 0.278 Angle : 0.727 8.645 13850 Z= 0.370 Chirality : 0.048 0.180 1570 Planarity : 0.004 0.030 1742 Dihedral : 5.027 23.012 1406 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.15 % Allowed : 14.39 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.22 (0.24), residues: 1274 helix: 0.58 (0.34), residues: 212 sheet: 0.22 (0.23), residues: 536 loop : -0.73 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 112 TYR 0.023 0.002 TYR C 177 PHE 0.016 0.002 PHE C 102 TRP 0.015 0.002 TRP D 47 HIS 0.004 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00678 (10134) covalent geometry : angle 0.72540 (13830) SS BOND : bond 0.00465 ( 10) SS BOND : angle 1.28694 ( 20) hydrogen bonds : bond 0.04267 ( 410) hydrogen bonds : angle 5.22629 ( 1076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.411 Fit side-chains REVERT: C 24 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7582 (mmm-85) REVERT: C 27 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: C 83 GLU cc_start: 0.8330 (mp0) cc_final: 0.8118 (mt-10) REVERT: C 107 LYS cc_start: 0.8655 (tttt) cc_final: 0.8313 (mtpm) REVERT: C 128 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7883 (tm-30) REVERT: C 158 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7051 (tm-30) REVERT: C 161 ASN cc_start: 0.8269 (p0) cc_final: 0.8003 (OUTLIER) REVERT: C 199 GLU cc_start: 0.7962 (tt0) cc_final: 0.7745 (tt0) REVERT: D 73 ASP cc_start: 0.8064 (t0) cc_final: 0.7597 (m-30) REVERT: D 74 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7360 (mtmm) REVERT: D 82 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: D 211 THR cc_start: 0.7118 (m) cc_final: 0.6808 (m) REVERT: E 12 THR cc_start: 0.9123 (t) cc_final: 0.8660 (m) REVERT: E 18 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7852 (ptp90) REVERT: E 107 LYS cc_start: 0.8714 (tttt) cc_final: 0.8313 (mtpm) REVERT: E 158 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7119 (tm-30) REVERT: F 20 ILE cc_start: 0.8777 (mt) cc_final: 0.8446 (mt) REVERT: F 74 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7225 (mtmm) REVERT: F 150 LYS cc_start: 0.7876 (tttm) cc_final: 0.7489 (ttpp) REVERT: F 211 THR cc_start: 0.7289 (m) cc_final: 0.6973 (m) REVERT: A 190 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7477 (t0) REVERT: A 205 LYS cc_start: 0.6749 (mttt) cc_final: 0.6317 (mttt) REVERT: B 190 ASP cc_start: 0.7688 (m-30) cc_final: 0.7430 (t0) REVERT: B 205 LYS cc_start: 0.6780 (mttt) cc_final: 0.6124 (mmtt) outliers start: 41 outliers final: 25 residues processed: 170 average time/residue: 0.6725 time to fit residues: 121.3251 Evaluate side-chains 175 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.0030 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.144675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093644 restraints weight = 39788.573| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.41 r_work: 0.3012 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10144 Z= 0.123 Angle : 0.611 8.586 13850 Z= 0.309 Chirality : 0.042 0.134 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.564 23.334 1406 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.32 % Allowed : 15.77 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.01 (0.24), residues: 1274 helix: 1.01 (0.35), residues: 210 sheet: 0.36 (0.24), residues: 534 loop : -0.69 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 112 TYR 0.011 0.001 TYR C 177 PHE 0.016 0.001 PHE E 32 TRP 0.012 0.001 TRP C 167 HIS 0.001 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00292 (10134) covalent geometry : angle 0.61088 (13830) SS BOND : bond 0.00220 ( 10) SS BOND : angle 0.65760 ( 20) hydrogen bonds : bond 0.03354 ( 410) hydrogen bonds : angle 4.85722 ( 1076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.354 Fit side-chains REVERT: C 27 GLU cc_start: 0.8633 (pt0) cc_final: 0.8268 (pm20) REVERT: C 83 GLU cc_start: 0.8270 (mp0) cc_final: 0.7845 (mt-10) REVERT: C 107 LYS cc_start: 0.8745 (tttt) cc_final: 0.8412 (mtpm) REVERT: C 128 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7833 (tm-30) REVERT: C 158 GLU cc_start: 0.8379 (mm-30) cc_final: 0.6857 (tm-30) REVERT: C 159 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8036 (mmm-85) REVERT: D 20 ILE cc_start: 0.8572 (mt) cc_final: 0.8333 (mp) REVERT: D 73 ASP cc_start: 0.8008 (t0) cc_final: 0.7480 (m-30) REVERT: D 74 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7356 (mtmm) REVERT: D 211 THR cc_start: 0.7166 (m) cc_final: 0.6854 (m) REVERT: E 12 THR cc_start: 0.9130 (t) cc_final: 0.8667 (m) REVERT: E 18 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7807 (ptp90) REVERT: E 83 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7726 (pm20) REVERT: E 107 LYS cc_start: 0.8646 (tttt) cc_final: 0.7666 (ttpt) REVERT: E 128 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: F 20 ILE cc_start: 0.8790 (mt) cc_final: 0.8309 (mp) REVERT: F 74 LYS cc_start: 0.7551 (mtpt) cc_final: 0.7093 (mtmm) REVERT: F 103 GLU cc_start: 0.8906 (pm20) cc_final: 0.8660 (pm20) REVERT: F 150 LYS cc_start: 0.7910 (tttm) cc_final: 0.7567 (ttpp) REVERT: F 211 THR cc_start: 0.7400 (m) cc_final: 0.7069 (m) REVERT: F 215 LYS cc_start: 0.7075 (tppp) cc_final: 0.6361 (tppt) REVERT: A 64 CYS cc_start: 0.7588 (t) cc_final: 0.7285 (m) REVERT: A 190 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7127 (t0) REVERT: A 205 LYS cc_start: 0.6695 (mttt) cc_final: 0.6174 (mmtt) outliers start: 32 outliers final: 17 residues processed: 170 average time/residue: 0.6596 time to fit residues: 119.1497 Evaluate side-chains 174 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 0.0050 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.090153 restraints weight = 59005.616| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.90 r_work: 0.2934 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10144 Z= 0.186 Angle : 0.652 9.174 13850 Z= 0.330 Chirality : 0.044 0.152 1570 Planarity : 0.004 0.031 1742 Dihedral : 4.706 22.939 1406 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.51 % Allowed : 15.77 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.01 (0.24), residues: 1274 helix: 0.93 (0.35), residues: 210 sheet: 0.34 (0.23), residues: 538 loop : -0.64 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 112 TYR 0.017 0.002 TYR E 177 PHE 0.015 0.002 PHE E 32 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00451 (10134) covalent geometry : angle 0.65142 (13830) SS BOND : bond 0.00368 ( 10) SS BOND : angle 0.96183 ( 20) hydrogen bonds : bond 0.03700 ( 410) hydrogen bonds : angle 4.93708 ( 1076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7746 (mmm-85) REVERT: C 27 GLU cc_start: 0.8644 (pt0) cc_final: 0.8276 (pm20) REVERT: C 83 GLU cc_start: 0.8332 (mp0) cc_final: 0.8123 (mt-10) REVERT: C 107 LYS cc_start: 0.8723 (tttt) cc_final: 0.8406 (mtpm) REVERT: C 128 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7862 (tm-30) REVERT: C 161 ASN cc_start: 0.8346 (p0) cc_final: 0.8010 (OUTLIER) REVERT: C 199 GLU cc_start: 0.7964 (tt0) cc_final: 0.7756 (tt0) REVERT: D 20 ILE cc_start: 0.8590 (mt) cc_final: 0.8315 (mp) REVERT: D 59 ASN cc_start: 0.8478 (m110) cc_final: 0.8270 (m110) REVERT: D 73 ASP cc_start: 0.8075 (t0) cc_final: 0.7512 (m-30) REVERT: D 74 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7394 (mtmm) REVERT: D 211 THR cc_start: 0.7109 (m) cc_final: 0.6789 (m) REVERT: E 12 THR cc_start: 0.9141 (t) cc_final: 0.8689 (m) REVERT: E 18 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7831 (ptp90) REVERT: E 107 LYS cc_start: 0.8725 (tttt) cc_final: 0.8337 (mtpm) REVERT: E 128 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: F 20 ILE cc_start: 0.8765 (mt) cc_final: 0.8276 (mp) REVERT: F 55 ASP cc_start: 0.8609 (p0) cc_final: 0.8364 (p0) REVERT: F 74 LYS cc_start: 0.7608 (mtpt) cc_final: 0.7106 (mtmm) REVERT: F 150 LYS cc_start: 0.7888 (tttm) cc_final: 0.7527 (ttpp) REVERT: F 211 THR cc_start: 0.7373 (m) cc_final: 0.7043 (m) REVERT: F 215 LYS cc_start: 0.7039 (tppp) cc_final: 0.6323 (tppt) REVERT: A 64 CYS cc_start: 0.7601 (t) cc_final: 0.7306 (m) REVERT: A 128 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8696 (mm) REVERT: A 190 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7365 (t0) REVERT: A 205 LYS cc_start: 0.6689 (mttt) cc_final: 0.6281 (mttt) REVERT: B 128 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8703 (mm) outliers start: 34 outliers final: 23 residues processed: 170 average time/residue: 0.6404 time to fit residues: 115.4673 Evaluate side-chains 173 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091147 restraints weight = 44021.130| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.51 r_work: 0.2969 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10144 Z= 0.168 Angle : 0.652 9.391 13850 Z= 0.329 Chirality : 0.044 0.149 1570 Planarity : 0.004 0.031 1742 Dihedral : 4.694 22.380 1406 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.14 % Allowed : 16.42 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 (0.24), residues: 1274 helix: 0.97 (0.35), residues: 210 sheet: 0.37 (0.24), residues: 538 loop : -0.62 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 112 TYR 0.017 0.002 TYR C 177 PHE 0.013 0.002 PHE E 32 TRP 0.012 0.001 TRP D 47 HIS 0.002 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00409 (10134) covalent geometry : angle 0.65189 (13830) SS BOND : bond 0.00350 ( 10) SS BOND : angle 0.87584 ( 20) hydrogen bonds : bond 0.03622 ( 410) hydrogen bonds : angle 4.91506 ( 1076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.365 Fit side-chains REVERT: C 24 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7734 (mmm-85) REVERT: C 27 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: C 83 GLU cc_start: 0.8325 (mp0) cc_final: 0.8104 (mt-10) REVERT: C 107 LYS cc_start: 0.8708 (tttt) cc_final: 0.8389 (mtpm) REVERT: C 128 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7800 (tm-30) REVERT: C 158 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7187 (tm-30) REVERT: C 161 ASN cc_start: 0.8298 (p0) cc_final: 0.7929 (OUTLIER) REVERT: D 20 ILE cc_start: 0.8562 (mt) cc_final: 0.8285 (mp) REVERT: D 73 ASP cc_start: 0.8068 (t0) cc_final: 0.7572 (m-30) REVERT: D 74 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7378 (mtmm) REVERT: D 211 THR cc_start: 0.7112 (m) cc_final: 0.6789 (m) REVERT: E 12 THR cc_start: 0.9133 (t) cc_final: 0.8681 (m) REVERT: E 18 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7837 (ptp90) REVERT: E 24 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7662 (mmm-85) REVERT: E 83 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7678 (pm20) REVERT: E 107 LYS cc_start: 0.8643 (tttt) cc_final: 0.7583 (ttpt) REVERT: E 128 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: E 158 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7052 (tp30) REVERT: F 20 ILE cc_start: 0.8797 (mt) cc_final: 0.8312 (mp) REVERT: F 55 ASP cc_start: 0.8587 (p0) cc_final: 0.8323 (p0) REVERT: F 150 LYS cc_start: 0.7869 (tttm) cc_final: 0.7511 (ttpp) REVERT: F 211 THR cc_start: 0.7265 (m) cc_final: 0.6938 (m) REVERT: F 215 LYS cc_start: 0.7066 (tppp) cc_final: 0.6348 (tppt) REVERT: A 128 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8689 (mm) REVERT: A 205 LYS cc_start: 0.6719 (mttt) cc_final: 0.6215 (mmtt) outliers start: 30 outliers final: 24 residues processed: 169 average time/residue: 0.6563 time to fit residues: 117.7227 Evaluate side-chains 174 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.092097 restraints weight = 48307.806| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.65 r_work: 0.2980 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10144 Z= 0.142 Angle : 0.635 9.659 13850 Z= 0.320 Chirality : 0.043 0.139 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.595 22.526 1406 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.51 % Allowed : 16.61 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.15 (0.25), residues: 1274 helix: 1.07 (0.35), residues: 210 sheet: 0.47 (0.24), residues: 536 loop : -0.62 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 112 TYR 0.015 0.001 TYR C 177 PHE 0.015 0.001 PHE E 32 TRP 0.011 0.001 TRP E 167 HIS 0.002 0.000 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00344 (10134) covalent geometry : angle 0.63455 (13830) SS BOND : bond 0.00324 ( 10) SS BOND : angle 0.77595 ( 20) hydrogen bonds : bond 0.03445 ( 410) hydrogen bonds : angle 4.81776 ( 1076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.269 Fit side-chains REVERT: C 24 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7721 (mmm-85) REVERT: C 27 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: C 72 ARG cc_start: 0.7840 (ptp90) cc_final: 0.7632 (ptp90) REVERT: C 107 LYS cc_start: 0.8695 (tttt) cc_final: 0.8383 (mtpm) REVERT: C 128 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7816 (tm-30) REVERT: C 161 ASN cc_start: 0.8291 (p0) cc_final: 0.7915 (OUTLIER) REVERT: D 20 ILE cc_start: 0.8536 (mt) cc_final: 0.8266 (mp) REVERT: D 73 ASP cc_start: 0.8022 (t0) cc_final: 0.7442 (m-30) REVERT: D 74 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7350 (mtmm) REVERT: D 82 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: D 211 THR cc_start: 0.6988 (m) cc_final: 0.6678 (m) REVERT: E 12 THR cc_start: 0.9117 (t) cc_final: 0.8667 (m) REVERT: E 18 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7811 (ptp90) REVERT: E 24 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7662 (mmm-85) REVERT: E 83 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7659 (pm20) REVERT: E 107 LYS cc_start: 0.8633 (tttt) cc_final: 0.7637 (ttpt) REVERT: E 128 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: E 158 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7068 (tm-30) REVERT: F 20 ILE cc_start: 0.8784 (mt) cc_final: 0.8303 (mp) REVERT: F 55 ASP cc_start: 0.8572 (p0) cc_final: 0.8229 (p0) REVERT: F 150 LYS cc_start: 0.7913 (tttm) cc_final: 0.7572 (ttpp) REVERT: F 211 THR cc_start: 0.7050 (m) cc_final: 0.6708 (m) REVERT: F 215 LYS cc_start: 0.7056 (tppp) cc_final: 0.6340 (tppt) REVERT: A 128 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8642 (mm) REVERT: A 190 ASP cc_start: 0.7488 (m-30) cc_final: 0.7263 (t0) REVERT: A 205 LYS cc_start: 0.6693 (mttt) cc_final: 0.6190 (mmtt) REVERT: B 128 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8642 (mm) outliers start: 34 outliers final: 25 residues processed: 167 average time/residue: 0.6483 time to fit residues: 114.8422 Evaluate side-chains 175 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091432 restraints weight = 54992.705| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.81 r_work: 0.2956 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10144 Z= 0.151 Angle : 0.644 9.603 13850 Z= 0.324 Chirality : 0.043 0.144 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.602 22.335 1406 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.32 % Allowed : 16.88 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.18 (0.25), residues: 1274 helix: 1.07 (0.35), residues: 210 sheet: 0.51 (0.24), residues: 536 loop : -0.61 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 72 TYR 0.016 0.001 TYR C 177 PHE 0.015 0.002 PHE E 32 TRP 0.010 0.001 TRP D 47 HIS 0.002 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00367 (10134) covalent geometry : angle 0.64403 (13830) SS BOND : bond 0.00358 ( 10) SS BOND : angle 0.80902 ( 20) hydrogen bonds : bond 0.03489 ( 410) hydrogen bonds : angle 4.80873 ( 1076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4584.19 seconds wall clock time: 78 minutes 32.30 seconds (4712.30 seconds total)