Starting phenix.real_space_refine on Sat Sep 12 11:59:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pwn_20508/09_2026/6pwn_20508.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pwn_20508/09_2026/6pwn_20508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pwn_20508/09_2026/6pwn_20508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pwn_20508/09_2026/6pwn_20508.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pwn_20508/09_2026/6pwn_20508.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pwn_20508/09_2026/6pwn_20508.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pwn_20508/09_2026/6pwn_20508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pwn_20508/09_2026/6pwn_20508.map" } resolution = 3.1 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 49 5.16 5 C 9954 2.51 5 N 2597 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15379 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "D" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "G" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'POV': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'POV': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.19, per 1000 atoms: 0.21 Number of scatterers: 15379 At special positions: 0 Unit cell: (101.08, 101.08, 147.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 7 15.00 O 2772 8.00 N 2597 7.00 C 9954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 537.9 milliseconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 54.3% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.935A pdb=" N VAL A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 58 Processing helix chain 'A' and resid 62 through 90 Processing helix chain 'A' and resid 93 through 128 removed outlier: 4.887A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 245 through 265 removed outlier: 3.630A pdb=" N ASP A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.936A pdb=" N VAL B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 58 Processing helix chain 'B' and resid 62 through 90 Processing helix chain 'B' and resid 93 through 128 removed outlier: 4.886A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.630A pdb=" N ASP B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.936A pdb=" N VAL C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 58 Processing helix chain 'C' and resid 62 through 90 Processing helix chain 'C' and resid 93 through 128 removed outlier: 4.886A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 245 through 265 removed outlier: 3.630A pdb=" N ASP C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.936A pdb=" N VAL D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 58 Processing helix chain 'D' and resid 62 through 90 Processing helix chain 'D' and resid 93 through 128 removed outlier: 4.887A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 245 through 265 removed outlier: 3.630A pdb=" N ASP D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 removed outlier: 3.937A pdb=" N VAL E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 58 Processing helix chain 'E' and resid 62 through 90 Processing helix chain 'E' and resid 93 through 128 removed outlier: 4.887A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER E 116 " --> pdb=" O GLN E 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 245 through 265 removed outlier: 3.630A pdb=" N ASP E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.936A pdb=" N VAL F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 58 Processing helix chain 'F' and resid 62 through 90 Processing helix chain 'F' and resid 93 through 128 removed outlier: 4.887A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER F 116 " --> pdb=" O GLN F 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 245 through 265 removed outlier: 3.629A pdb=" N ASP F 262 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.937A pdb=" N VAL G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 58 Processing helix chain 'G' and resid 62 through 90 Processing helix chain 'G' and resid 93 through 128 removed outlier: 4.887A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 116 " --> pdb=" O GLN G 112 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 245 through 265 removed outlier: 3.630A pdb=" N ASP G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.777A pdb=" N VAL A 136 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 136 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE B 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 136 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE C 162 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 136 " --> pdb=" O GLY D 143 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL E 136 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE E 162 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 136 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE F 162 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL G 136 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE G 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 3.720A pdb=" N VAL A 239 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279 removed outlier: 7.184A pdb=" N MET A 273 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LYS B 278 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 275 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET B 273 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS C 278 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 275 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET C 273 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LYS D 278 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL C 275 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N MET D 273 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LYS E 278 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 275 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N MET E 273 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LYS F 278 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL E 275 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET F 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LYS G 278 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL F 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 278 " --> pdb=" O VAL G 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 3.720A pdb=" N VAL B 239 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 3.720A pdb=" N VAL C 239 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 3.719A pdb=" N VAL D 239 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 3.720A pdb=" N VAL E 239 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 3.719A pdb=" N VAL F 239 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 3.719A pdb=" N VAL G 239 " --> pdb=" O ASN G 186 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2997 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: 2.25 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2499 1.31 - 1.43: 3658 1.43 - 1.56: 9124 1.56 - 1.68: 168 1.68 - 1.80: 105 Bond restraints: 15554 Sorted by residual: bond pdb=" C31 POV F 301 " pdb=" O31 POV F 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C31 POV C 301 " pdb=" O31 POV C 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C31 POV A 301 " pdb=" O31 POV A 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C31 POV E 301 " pdb=" O31 POV E 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C31 POV B 301 " pdb=" O31 POV B 301 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 15549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 20517 2.32 - 4.64: 370 4.64 - 6.96: 57 6.96 - 9.27: 28 9.27 - 11.59: 21 Bond angle restraints: 20993 Sorted by residual: angle pdb=" O13 POV B 301 " pdb=" P POV B 301 " pdb=" O14 POV B 301 " ideal model delta sigma weight residual 121.11 109.52 11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O13 POV F 301 " pdb=" P POV F 301 " pdb=" O14 POV F 301 " ideal model delta sigma weight residual 121.11 109.53 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O13 POV G 301 " pdb=" P POV G 301 " pdb=" O14 POV G 301 " ideal model delta sigma weight residual 121.11 109.53 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O11 POV F 301 " pdb=" P POV F 301 " pdb=" O12 POV F 301 " ideal model delta sigma weight residual 97.67 109.24 -11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O13 POV D 301 " pdb=" P POV D 301 " pdb=" O14 POV D 301 " ideal model delta sigma weight residual 121.11 109.55 11.56 3.00e+00 1.11e-01 1.49e+01 ... (remaining 20988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 8322 16.00 - 32.00: 826 32.00 - 48.00: 183 48.00 - 64.00: 42 64.00 - 80.00: 28 Dihedral angle restraints: 9401 sinusoidal: 3794 harmonic: 5607 Sorted by residual: dihedral pdb=" CA ASP D 8 " pdb=" CB ASP D 8 " pdb=" CG ASP D 8 " pdb=" OD1 ASP D 8 " ideal model delta sinusoidal sigma weight residual -30.00 -88.70 58.70 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP F 8 " pdb=" CB ASP F 8 " pdb=" CG ASP F 8 " pdb=" OD1 ASP F 8 " ideal model delta sinusoidal sigma weight residual -30.00 -88.70 58.70 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP E 8 " pdb=" CB ASP E 8 " pdb=" CG ASP E 8 " pdb=" OD1 ASP E 8 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 9398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1246 0.027 - 0.054: 788 0.054 - 0.081: 251 0.081 - 0.108: 171 0.108 - 0.135: 64 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CB ILE A 165 " pdb=" CA ILE A 165 " pdb=" CG1 ILE A 165 " pdb=" CG2 ILE A 165 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CB ILE E 165 " pdb=" CA ILE E 165 " pdb=" CG1 ILE E 165 " pdb=" CG2 ILE E 165 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CB ILE D 165 " pdb=" CA ILE D 165 " pdb=" CG1 ILE D 165 " pdb=" CG2 ILE D 165 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2517 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER G 9 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C SER G 9 " 0.030 2.00e-02 2.50e+03 pdb=" O SER G 9 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE G 10 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 9 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C SER B 9 " -0.030 2.00e-02 2.50e+03 pdb=" O SER B 9 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE B 10 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 9 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C SER A 9 " -0.030 2.00e-02 2.50e+03 pdb=" O SER A 9 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 10 " 0.010 2.00e-02 2.50e+03 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3880 2.80 - 3.33: 15525 3.33 - 3.85: 23789 3.85 - 4.38: 28368 4.38 - 4.90: 49171 Nonbonded interactions: 120733 Sorted by model distance: nonbonded pdb=" OE2 GLU A 134 " pdb=" ND2 ASN A 177 " model vdw 2.276 3.120 nonbonded pdb=" OE2 GLU F 134 " pdb=" ND2 ASN F 177 " model vdw 2.276 3.120 nonbonded pdb=" OE2 GLU C 134 " pdb=" ND2 ASN C 177 " model vdw 2.276 3.120 nonbonded pdb=" OE2 GLU G 134 " pdb=" ND2 ASN G 177 " model vdw 2.277 3.120 nonbonded pdb=" OE2 GLU E 134 " pdb=" ND2 ASN E 177 " model vdw 2.277 3.120 ... (remaining 120728 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 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.008 0.103 15554 Z= 0.414 Angle : 0.862 11.592 20993 Z= 0.404 Chirality : 0.044 0.135 2520 Planarity : 0.003 0.019 2625 Dihedral : 14.345 80.003 5789 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.44 % Allowed : 5.29 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.17), residues: 1946 helix: -0.48 (0.15), residues: 1008 sheet: -1.57 (0.31), residues: 273 loop : -2.75 (0.19), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 88 TYR 0.008 0.001 TYR B 250 PHE 0.008 0.001 PHE F 68 TRP 0.005 0.001 TRP A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00846 / 0.41 (15554) covalent geometry : angle 0.86159 / 0.40 (20993) hydrogen bonds : bond 0.15611 / 10.66 ( 1020) hydrogen bonds : angle 6.55075 / 4.63 ( 2997) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 235 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7663 (mtm) cc_final: 0.7425 (mmp) REVERT: A 112 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8811 (tm-30) REVERT: B 112 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8743 (tm-30) REVERT: B 134 GLU cc_start: 0.8154 (tt0) cc_final: 0.7732 (tt0) REVERT: C 10 ILE cc_start: 0.4654 (OUTLIER) cc_final: 0.4299 (tp) REVERT: C 21 GLN cc_start: 0.9047 (pt0) cc_final: 0.8820 (pt0) REVERT: C 112 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8908 (tm-30) REVERT: C 220 GLU cc_start: 0.8153 (pp20) cc_final: 0.7866 (pp20) REVERT: D 92 GLN cc_start: 0.8917 (mm110) cc_final: 0.8102 (tt0) REVERT: D 112 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8792 (tm-30) REVERT: D 220 GLU cc_start: 0.8180 (pp20) cc_final: 0.7915 (pp20) REVERT: E 75 TYR cc_start: 0.8258 (m-10) cc_final: 0.8038 (m-80) REVERT: E 92 GLN cc_start: 0.8910 (mm110) cc_final: 0.8121 (tt0) REVERT: E 112 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8890 (tm-30) REVERT: E 220 GLU cc_start: 0.8184 (pp20) cc_final: 0.7844 (pp20) REVERT: F 112 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8805 (tm-30) REVERT: F 134 GLU cc_start: 0.8151 (tt0) cc_final: 0.7921 (tt0) REVERT: F 203 GLN cc_start: 0.8039 (tp40) cc_final: 0.7560 (tm-30) REVERT: F 212 GLU cc_start: 0.7956 (tp30) cc_final: 0.7647 (tp30) REVERT: F 220 GLU cc_start: 0.8204 (pp20) cc_final: 0.7910 (pp20) REVERT: G 21 GLN cc_start: 0.9083 (pt0) cc_final: 0.8869 (pt0) REVERT: G 92 GLN cc_start: 0.8851 (mm110) cc_final: 0.7987 (tt0) REVERT: G 202 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8524 (mtpt) outliers start: 7 outliers final: 0 residues processed: 242 average time/residue: 0.1518 time to fit residues: 51.3953 Evaluate side-chains 187 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN D 21 GLN D 92 GLN E 21 GLN E 92 GLN F 21 GLN G 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.063748 restraints weight = 33160.988| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.83 r_work: 0.2816 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15554 Z= 0.224 Angle : 0.579 7.044 20993 Z= 0.305 Chirality : 0.044 0.171 2520 Planarity : 0.004 0.028 2625 Dihedral : 11.589 77.439 2473 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.38 % Allowed : 10.76 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.18), residues: 1946 helix: 0.59 (0.16), residues: 1064 sheet: -0.57 (0.34), residues: 273 loop : -2.23 (0.21), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 131 TYR 0.009 0.001 TYR D 250 PHE 0.008 0.001 PHE A 178 TRP 0.009 0.001 TRP G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 (15554) covalent geometry : angle 0.57911 / 0.31 (20993) hydrogen bonds : bond 0.04856 / 3.30 ( 1020) hydrogen bonds : angle 4.73630 / 3.36 ( 2997) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7976 (mtm) cc_final: 0.7615 (mmp) REVERT: A 112 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8882 (tm-30) REVERT: A 255 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 112 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8876 (tm-30) REVERT: B 203 GLN cc_start: 0.8431 (tp40) cc_final: 0.8123 (tm-30) REVERT: B 212 GLU cc_start: 0.8038 (tp30) cc_final: 0.7803 (tp30) REVERT: B 278 LYS cc_start: 0.8491 (ptmt) cc_final: 0.7874 (pttt) REVERT: C 21 GLN cc_start: 0.9331 (pt0) cc_final: 0.9095 (pt0) REVERT: C 202 LYS cc_start: 0.8753 (mtpt) cc_final: 0.8435 (mtpp) REVERT: D 92 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8206 (tt0) REVERT: D 112 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8949 (tm-30) REVERT: D 255 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8278 (tm-30) REVERT: D 278 LYS cc_start: 0.8267 (ptmt) cc_final: 0.7630 (ptpt) REVERT: E 75 TYR cc_start: 0.8285 (m-10) cc_final: 0.8060 (m-80) REVERT: E 278 LYS cc_start: 0.8380 (ptmt) cc_final: 0.7622 (ptpt) REVERT: F 112 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8891 (tm-30) REVERT: F 203 GLN cc_start: 0.8319 (tp40) cc_final: 0.7756 (tm-30) REVERT: G 20 ASN cc_start: 0.8946 (t0) cc_final: 0.8735 (t0) REVERT: G 47 MET cc_start: 0.7082 (mmp) cc_final: 0.6866 (mmp) REVERT: G 92 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8050 (tt0) REVERT: G 255 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: G 278 LYS cc_start: 0.8249 (ptmt) cc_final: 0.7913 (ptpt) outliers start: 22 outliers final: 14 residues processed: 223 average time/residue: 0.1280 time to fit residues: 40.9687 Evaluate side-chains 197 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 53 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 186 optimal weight: 0.0470 chunk 158 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 21 GLN B 11 ASN B 21 GLN E 21 GLN F 21 GLN ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.066975 restraints weight = 33060.242| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.89 r_work: 0.2880 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15554 Z= 0.102 Angle : 0.479 5.011 20993 Z= 0.255 Chirality : 0.041 0.165 2520 Planarity : 0.002 0.019 2625 Dihedral : 10.593 68.921 2471 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.39 % Allowed : 10.32 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1946 helix: 1.49 (0.16), residues: 1050 sheet: 0.08 (0.34), residues: 273 loop : -1.77 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 279 TYR 0.004 0.001 TYR G 27 PHE 0.008 0.001 PHE A 277 TRP 0.021 0.001 TRP C 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (15554) covalent geometry : angle 0.47882 / 0.26 (20993) hydrogen bonds : bond 0.03781 / 2.58 ( 1020) hydrogen bonds : angle 4.11145 / 2.92 ( 2997) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6288 (tpt) cc_final: 0.5933 (tpt) REVERT: A 112 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8748 (tm-30) REVERT: A 203 GLN cc_start: 0.8210 (tp40) cc_final: 0.7961 (tp40) REVERT: B 203 GLN cc_start: 0.8368 (tp40) cc_final: 0.7848 (tm-30) REVERT: B 278 LYS cc_start: 0.8491 (ptmt) cc_final: 0.7878 (pttt) REVERT: C 1 MET cc_start: 0.6387 (tpp) cc_final: 0.6160 (tpp) REVERT: C 278 LYS cc_start: 0.8519 (ptpt) cc_final: 0.7972 (pttt) REVERT: D 1 MET cc_start: 0.6130 (mmm) cc_final: 0.5905 (tpp) REVERT: D 92 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8107 (tt0) REVERT: D 112 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8852 (tm-30) REVERT: D 202 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8427 (mtpt) REVERT: D 203 GLN cc_start: 0.8267 (tp40) cc_final: 0.7592 (tm-30) REVERT: D 212 GLU cc_start: 0.7795 (tp30) cc_final: 0.7591 (tp30) REVERT: E 75 TYR cc_start: 0.8213 (m-10) cc_final: 0.7967 (m-80) REVERT: E 97 ILE cc_start: 0.8855 (pt) cc_final: 0.8644 (mp) REVERT: F 38 ILE cc_start: 0.8992 (mt) cc_final: 0.8724 (mm) REVERT: F 203 GLN cc_start: 0.8204 (tp40) cc_final: 0.7681 (tm-30) REVERT: G 75 TYR cc_start: 0.7981 (m-10) cc_final: 0.7761 (m-10) REVERT: G 92 GLN cc_start: 0.8905 (mm-40) cc_final: 0.7984 (tt0) REVERT: G 155 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8547 (ptm) REVERT: G 255 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8416 (tm-30) outliers start: 38 outliers final: 14 residues processed: 253 average time/residue: 0.1302 time to fit residues: 48.2608 Evaluate side-chains 205 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 170 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN B 21 GLN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 ASN ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN G 11 ASN G 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066958 restraints weight = 32560.161| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.68 r_work: 0.2910 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15554 Z= 0.116 Angle : 0.492 6.952 20993 Z= 0.262 Chirality : 0.041 0.151 2520 Planarity : 0.002 0.020 2625 Dihedral : 10.270 65.252 2471 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.01 % Allowed : 11.83 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1946 helix: 1.70 (0.16), residues: 1050 sheet: 0.38 (0.33), residues: 273 loop : -1.51 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 279 TYR 0.007 0.001 TYR C 250 PHE 0.010 0.001 PHE G 127 TRP 0.016 0.001 TRP F 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (15554) covalent geometry : angle 0.49180 / 0.26 (20993) hydrogen bonds : bond 0.03768 / 2.57 ( 1020) hydrogen bonds : angle 4.05186 / 2.89 ( 2997) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6267 (tpt) cc_final: 0.6029 (tpt) REVERT: A 112 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 203 GLN cc_start: 0.8137 (tp40) cc_final: 0.7886 (tp40) REVERT: B 112 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8718 (pp30) REVERT: B 203 GLN cc_start: 0.8380 (tp40) cc_final: 0.7865 (tm-30) REVERT: B 212 GLU cc_start: 0.8017 (tp30) cc_final: 0.7333 (tp30) REVERT: B 278 LYS cc_start: 0.8474 (ptmt) cc_final: 0.7876 (pttt) REVERT: C 92 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8014 (tt0) REVERT: C 203 GLN cc_start: 0.8377 (tp40) cc_final: 0.8101 (tp40) REVERT: C 278 LYS cc_start: 0.8551 (ptpt) cc_final: 0.8005 (pttt) REVERT: D 92 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8112 (tt0) REVERT: D 112 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8841 (tm-30) REVERT: D 202 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8474 (mtpt) REVERT: D 203 GLN cc_start: 0.8291 (tp40) cc_final: 0.7630 (tm-30) REVERT: D 212 GLU cc_start: 0.7831 (tp30) cc_final: 0.7579 (tp30) REVERT: E 68 PHE cc_start: 0.8003 (m-80) cc_final: 0.7716 (m-10) REVERT: E 75 TYR cc_start: 0.8137 (m-10) cc_final: 0.7877 (m-80) REVERT: F 112 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8705 (pp30) REVERT: F 203 GLN cc_start: 0.8213 (tp40) cc_final: 0.7869 (tm-30) REVERT: G 1 MET cc_start: 0.6445 (tpt) cc_final: 0.6174 (tpt) REVERT: G 21 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8846 (mt0) REVERT: G 75 TYR cc_start: 0.7964 (m-10) cc_final: 0.7743 (m-10) REVERT: G 92 GLN cc_start: 0.8884 (mm-40) cc_final: 0.7970 (tt0) REVERT: G 112 GLN cc_start: 0.8989 (pp30) cc_final: 0.8487 (pp30) REVERT: G 255 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8391 (tm-30) outliers start: 32 outliers final: 15 residues processed: 226 average time/residue: 0.1272 time to fit residues: 42.1003 Evaluate side-chains 202 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 0.0060 chunk 99 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 111 optimal weight: 0.0970 chunk 185 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN B 21 GLN C 11 ASN C 21 GLN D 21 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN F 21 GLN G 21 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.096561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066760 restraints weight = 32617.345| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.67 r_work: 0.2903 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15554 Z= 0.128 Angle : 0.489 8.121 20993 Z= 0.260 Chirality : 0.041 0.159 2520 Planarity : 0.002 0.020 2625 Dihedral : 10.072 62.886 2471 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.01 % Allowed : 12.71 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 1946 helix: 1.87 (0.16), residues: 1043 sheet: 0.46 (0.33), residues: 273 loop : -1.40 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 279 TYR 0.007 0.001 TYR C 250 PHE 0.006 0.001 PHE A 277 TRP 0.006 0.001 TRP F 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (15554) covalent geometry : angle 0.48867 / 0.26 (20993) hydrogen bonds : bond 0.03804 / 2.60 ( 1020) hydrogen bonds : angle 4.00084 / 2.86 ( 2997) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6038 (tpt) cc_final: 0.5671 (tpp) REVERT: A 112 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8777 (tm-30) REVERT: A 203 GLN cc_start: 0.8194 (tp40) cc_final: 0.7923 (tp40) REVERT: B 1 MET cc_start: 0.6611 (tpt) cc_final: 0.6382 (tpt) REVERT: B 203 GLN cc_start: 0.8387 (tp40) cc_final: 0.8150 (tm-30) REVERT: B 212 GLU cc_start: 0.7902 (tp30) cc_final: 0.7427 (tp30) REVERT: B 278 LYS cc_start: 0.8466 (ptmt) cc_final: 0.7879 (pttt) REVERT: C 1 MET cc_start: 0.6590 (tpp) cc_final: 0.6246 (tpp) REVERT: C 92 GLN cc_start: 0.8991 (mm-40) cc_final: 0.7997 (tt0) REVERT: C 203 GLN cc_start: 0.8398 (tp40) cc_final: 0.8127 (tp40) REVERT: D 1 MET cc_start: 0.6682 (tpt) cc_final: 0.5963 (tpt) REVERT: D 21 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8270 (mp10) REVERT: D 92 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8139 (tt0) REVERT: D 112 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8847 (tm-30) REVERT: D 202 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8450 (mtpt) REVERT: D 203 GLN cc_start: 0.8350 (tp40) cc_final: 0.7676 (tm-30) REVERT: D 212 GLU cc_start: 0.7855 (tp30) cc_final: 0.7539 (tp30) REVERT: D 278 LYS cc_start: 0.8228 (ptmt) cc_final: 0.7705 (ptpt) REVERT: E 47 MET cc_start: 0.7303 (mmp) cc_final: 0.7042 (mmp) REVERT: E 68 PHE cc_start: 0.8010 (m-80) cc_final: 0.7733 (m-10) REVERT: E 75 TYR cc_start: 0.8117 (m-10) cc_final: 0.7865 (m-80) REVERT: E 92 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8012 (tt0) REVERT: F 112 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8744 (pp30) REVERT: F 203 GLN cc_start: 0.8233 (tp40) cc_final: 0.7908 (tm-30) REVERT: G 1 MET cc_start: 0.6387 (tpt) cc_final: 0.6157 (tpt) REVERT: G 21 GLN cc_start: 0.9093 (pt0) cc_final: 0.8888 (mt0) REVERT: G 75 TYR cc_start: 0.7917 (m-10) cc_final: 0.7702 (m-10) REVERT: G 112 GLN cc_start: 0.9039 (pp30) cc_final: 0.8547 (pp30) REVERT: G 255 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8378 (tm-30) outliers start: 32 outliers final: 17 residues processed: 213 average time/residue: 0.1344 time to fit residues: 42.1199 Evaluate side-chains 199 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 84 optimal weight: 30.0000 chunk 156 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN B 21 GLN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN E 11 ASN E 21 GLN F 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064379 restraints weight = 32959.558| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.63 r_work: 0.2859 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15554 Z= 0.237 Angle : 0.556 7.697 20993 Z= 0.296 Chirality : 0.043 0.140 2520 Planarity : 0.003 0.030 2625 Dihedral : 10.384 65.086 2471 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.77 % Allowed : 13.47 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1946 helix: 1.50 (0.16), residues: 1071 sheet: 0.38 (0.33), residues: 273 loop : -1.47 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 279 TYR 0.014 0.001 TYR C 250 PHE 0.008 0.001 PHE G 130 TRP 0.005 0.001 TRP E 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 (15554) covalent geometry : angle 0.55607 / 0.30 (20993) hydrogen bonds : bond 0.04504 / 3.05 ( 1020) hydrogen bonds : angle 4.34135 / 3.09 ( 2997) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6246 (tpt) cc_final: 0.5956 (tpt) REVERT: A 203 GLN cc_start: 0.8355 (tp40) cc_final: 0.8088 (tm-30) REVERT: B 203 GLN cc_start: 0.8538 (tp40) cc_final: 0.8289 (tm-30) REVERT: B 212 GLU cc_start: 0.8037 (tp30) cc_final: 0.7577 (tp30) REVERT: B 278 LYS cc_start: 0.8459 (ptmt) cc_final: 0.7894 (pttt) REVERT: C 21 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8395 (mp10) REVERT: D 1 MET cc_start: 0.6864 (tpt) cc_final: 0.6171 (tpt) REVERT: D 92 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8180 (tt0) REVERT: D 112 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8901 (tm-30) REVERT: D 202 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8503 (mtpt) REVERT: D 203 GLN cc_start: 0.8444 (tp40) cc_final: 0.8044 (tm-30) REVERT: D 278 LYS cc_start: 0.8149 (ptmt) cc_final: 0.7476 (ptpt) REVERT: E 21 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8421 (mp10) REVERT: E 75 TYR cc_start: 0.8198 (m-10) cc_final: 0.7956 (m-10) REVERT: E 92 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8202 (tt0) REVERT: E 169 LYS cc_start: 0.9231 (ttpt) cc_final: 0.9010 (ttpt) REVERT: F 203 GLN cc_start: 0.8341 (tp40) cc_final: 0.7922 (tm-30) REVERT: G 1 MET cc_start: 0.6403 (tpt) cc_final: 0.6121 (tpt) REVERT: G 112 GLN cc_start: 0.9173 (pp30) cc_final: 0.8823 (pp30) REVERT: G 203 GLN cc_start: 0.8476 (tp40) cc_final: 0.8265 (tp40) REVERT: G 255 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8395 (tm-30) outliers start: 44 outliers final: 28 residues processed: 206 average time/residue: 0.1271 time to fit residues: 38.2794 Evaluate side-chains 207 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 134 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN B 21 GLN C 21 GLN D 21 GLN E 21 GLN E 203 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.066201 restraints weight = 32648.948| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.67 r_work: 0.2893 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15554 Z= 0.133 Angle : 0.492 7.623 20993 Z= 0.261 Chirality : 0.041 0.160 2520 Planarity : 0.002 0.022 2625 Dihedral : 10.000 64.659 2471 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.39 % Allowed : 14.03 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1946 helix: 1.76 (0.16), residues: 1071 sheet: 0.49 (0.33), residues: 273 loop : -1.29 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 279 TYR 0.007 0.001 TYR D 250 PHE 0.006 0.001 PHE G 127 TRP 0.005 0.001 TRP F 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (15554) covalent geometry : angle 0.49159 / 0.26 (20993) hydrogen bonds : bond 0.03903 / 2.66 ( 1020) hydrogen bonds : angle 4.01687 / 2.86 ( 2997) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6016 (tpt) cc_final: 0.5675 (tpt) REVERT: A 21 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8499 (mp10) REVERT: A 203 GLN cc_start: 0.8237 (tp40) cc_final: 0.7960 (tp40) REVERT: B 60 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6183 (pttm) REVERT: B 203 GLN cc_start: 0.8418 (tp40) cc_final: 0.7882 (tm-30) REVERT: B 212 GLU cc_start: 0.7867 (tp30) cc_final: 0.7477 (tp30) REVERT: B 278 LYS cc_start: 0.8432 (ptmt) cc_final: 0.7970 (pttt) REVERT: C 92 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8066 (tt0) REVERT: C 134 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: D 1 MET cc_start: 0.6569 (tpt) cc_final: 0.5800 (tpt) REVERT: D 21 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: D 92 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8125 (tt0) REVERT: D 112 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8881 (tm-30) REVERT: D 202 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8416 (mtpt) REVERT: D 203 GLN cc_start: 0.8361 (tp40) cc_final: 0.7921 (tm-30) REVERT: D 278 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7466 (ptpt) REVERT: E 21 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: E 75 TYR cc_start: 0.8123 (m-10) cc_final: 0.7875 (m-80) REVERT: E 92 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8040 (tt0) REVERT: F 21 GLN cc_start: 0.9067 (pt0) cc_final: 0.8477 (mp10) REVERT: F 203 GLN cc_start: 0.8273 (tp40) cc_final: 0.7851 (tm-30) REVERT: G 1 MET cc_start: 0.6203 (tpt) cc_final: 0.5945 (tpt) REVERT: G 21 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: G 112 GLN cc_start: 0.9143 (pp30) cc_final: 0.8757 (pp30) REVERT: G 203 GLN cc_start: 0.8376 (tp40) cc_final: 0.8158 (tp40) REVERT: G 255 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8373 (tm-30) outliers start: 38 outliers final: 17 residues processed: 217 average time/residue: 0.1206 time to fit residues: 38.7217 Evaluate side-chains 204 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 139 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN B 21 GLN C 21 GLN ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN E 203 GLN F 21 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.096907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067250 restraints weight = 32899.257| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.70 r_work: 0.2914 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15554 Z= 0.108 Angle : 0.485 6.898 20993 Z= 0.257 Chirality : 0.041 0.171 2520 Planarity : 0.002 0.021 2625 Dihedral : 9.774 61.812 2471 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.39 % Allowed : 14.03 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.19), residues: 1946 helix: 1.95 (0.16), residues: 1071 sheet: 0.57 (0.33), residues: 273 loop : -1.20 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.005 0.001 TYR C 250 PHE 0.007 0.001 PHE G 127 TRP 0.004 0.001 TRP G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (15554) covalent geometry : angle 0.48489 / 0.26 (20993) hydrogen bonds : bond 0.03741 / 2.56 ( 1020) hydrogen bonds : angle 3.90392 / 2.79 ( 2997) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5916 (tpt) cc_final: 0.5619 (tpt) REVERT: A 21 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: A 112 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8716 (pp30) REVERT: A 203 GLN cc_start: 0.8169 (tp40) cc_final: 0.7898 (tp40) REVERT: B 56 MET cc_start: 0.8062 (ppp) cc_final: 0.7787 (ppp) REVERT: B 112 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8670 (pp30) REVERT: B 203 GLN cc_start: 0.8381 (tp40) cc_final: 0.7862 (tm-30) REVERT: B 212 GLU cc_start: 0.7832 (tp30) cc_final: 0.7423 (tp30) REVERT: B 278 LYS cc_start: 0.8427 (ptmt) cc_final: 0.8010 (pttt) REVERT: C 21 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.9044 (mt0) REVERT: C 92 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8044 (tt0) REVERT: C 134 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: C 203 GLN cc_start: 0.8320 (tp40) cc_final: 0.8035 (tp40) REVERT: D 1 MET cc_start: 0.6436 (tpt) cc_final: 0.5609 (tpt) REVERT: D 21 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8279 (mp10) REVERT: D 92 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8073 (tt0) REVERT: D 112 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8838 (tm-30) REVERT: D 202 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8404 (mtpt) REVERT: D 203 GLN cc_start: 0.8346 (tp40) cc_final: 0.7666 (tm-30) REVERT: D 212 GLU cc_start: 0.7876 (tp30) cc_final: 0.7562 (tp30) REVERT: D 278 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7499 (ptpt) REVERT: E 56 MET cc_start: 0.8137 (ppp) cc_final: 0.7841 (ppp) REVERT: E 75 TYR cc_start: 0.8029 (m-10) cc_final: 0.7776 (m-80) REVERT: E 92 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8217 (tt0) REVERT: E 112 GLN cc_start: 0.9006 (pp30) cc_final: 0.8801 (pp30) REVERT: F 21 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8707 (mp10) REVERT: F 56 MET cc_start: 0.8171 (ppp) cc_final: 0.7877 (ppp) REVERT: F 134 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: F 203 GLN cc_start: 0.8203 (tp40) cc_final: 0.7780 (tm-30) REVERT: G 1 MET cc_start: 0.6209 (tpt) cc_final: 0.5973 (tpt) REVERT: G 112 GLN cc_start: 0.9086 (pp30) cc_final: 0.8682 (pp30) REVERT: G 255 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8382 (tm-30) outliers start: 38 outliers final: 17 residues processed: 218 average time/residue: 0.1246 time to fit residues: 40.0251 Evaluate side-chains 206 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN E 203 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.097042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.067412 restraints weight = 32632.034| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.67 r_work: 0.2919 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15554 Z= 0.111 Angle : 0.493 7.449 20993 Z= 0.259 Chirality : 0.041 0.179 2520 Planarity : 0.002 0.021 2625 Dihedral : 9.616 59.341 2471 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.64 % Allowed : 15.10 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 1946 helix: 2.01 (0.16), residues: 1071 sheet: 0.58 (0.33), residues: 259 loop : -1.03 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 279 TYR 0.006 0.001 TYR D 250 PHE 0.007 0.001 PHE G 127 TRP 0.005 0.000 TRP G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (15554) covalent geometry : angle 0.49304 / 0.26 (20993) hydrogen bonds : bond 0.03730 / 2.55 ( 1020) hydrogen bonds : angle 3.87869 / 2.78 ( 2997) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5749 (tpt) cc_final: 0.5418 (tpt) REVERT: A 21 GLN cc_start: 0.9124 (mt0) cc_final: 0.8298 (mp10) REVERT: A 112 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8706 (pp30) REVERT: A 203 GLN cc_start: 0.8164 (tp40) cc_final: 0.7942 (tm-30) REVERT: B 56 MET cc_start: 0.8203 (ppp) cc_final: 0.7944 (ppp) REVERT: B 112 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8648 (pp30) REVERT: B 203 GLN cc_start: 0.8389 (tp40) cc_final: 0.7871 (tm-30) REVERT: B 212 GLU cc_start: 0.7821 (tp30) cc_final: 0.7396 (tp30) REVERT: B 278 LYS cc_start: 0.8412 (ptmt) cc_final: 0.7997 (pttt) REVERT: C 21 GLN cc_start: 0.9226 (pt0) cc_final: 0.8754 (mp10) REVERT: C 56 MET cc_start: 0.8062 (ppp) cc_final: 0.7774 (ppp) REVERT: C 92 GLN cc_start: 0.8994 (mm-40) cc_final: 0.7964 (tt0) REVERT: C 134 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: C 203 GLN cc_start: 0.8327 (tp40) cc_final: 0.8028 (tp40) REVERT: C 278 LYS cc_start: 0.8523 (ptpt) cc_final: 0.7974 (ptpt) REVERT: D 1 MET cc_start: 0.6348 (tpt) cc_final: 0.5917 (tpt) REVERT: D 92 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8079 (tt0) REVERT: D 112 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8788 (tm-30) REVERT: D 202 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8405 (mtpt) REVERT: D 203 GLN cc_start: 0.8337 (tp40) cc_final: 0.7683 (tm-30) REVERT: D 212 GLU cc_start: 0.7899 (tp30) cc_final: 0.7550 (tp30) REVERT: D 278 LYS cc_start: 0.8055 (ptmt) cc_final: 0.7387 (ptpt) REVERT: E 56 MET cc_start: 0.8144 (ppp) cc_final: 0.7877 (ppp) REVERT: E 68 PHE cc_start: 0.8008 (m-80) cc_final: 0.7734 (m-10) REVERT: E 75 TYR cc_start: 0.7969 (m-10) cc_final: 0.7728 (m-80) REVERT: E 92 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8294 (tt0) REVERT: E 112 GLN cc_start: 0.8985 (pp30) cc_final: 0.8723 (pp30) REVERT: F 21 GLN cc_start: 0.9131 (pt0) cc_final: 0.8461 (mp10) REVERT: F 56 MET cc_start: 0.8113 (ppp) cc_final: 0.7834 (ppp) REVERT: F 134 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: F 203 GLN cc_start: 0.8233 (tp40) cc_final: 0.7820 (tm-30) REVERT: G 1 MET cc_start: 0.6179 (tpt) cc_final: 0.5909 (tpt) REVERT: G 21 GLN cc_start: 0.9193 (mt0) cc_final: 0.8617 (mp10) REVERT: G 92 GLN cc_start: 0.8879 (mm-40) cc_final: 0.7982 (tt0) REVERT: G 112 GLN cc_start: 0.9063 (pp30) cc_final: 0.8639 (pp30) REVERT: G 134 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: G 255 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8385 (tm-30) outliers start: 26 outliers final: 18 residues processed: 208 average time/residue: 0.1360 time to fit residues: 41.2221 Evaluate side-chains 208 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 119 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN C 21 GLN D 21 GLN E 21 GLN E 203 GLN F 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066307 restraints weight = 32976.725| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.70 r_work: 0.2897 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15554 Z= 0.150 Angle : 0.520 9.757 20993 Z= 0.273 Chirality : 0.042 0.183 2520 Planarity : 0.003 0.021 2625 Dihedral : 9.652 59.991 2471 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.95 % Allowed : 14.98 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.19), residues: 1946 helix: 1.93 (0.16), residues: 1071 sheet: 0.64 (0.33), residues: 273 loop : -1.20 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 279 TYR 0.010 0.001 TYR D 250 PHE 0.007 0.001 PHE G 127 TRP 0.003 0.001 TRP G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (15554) covalent geometry : angle 0.51987 / 0.27 (20993) hydrogen bonds : bond 0.03971 / 2.70 ( 1020) hydrogen bonds : angle 4.02474 / 2.87 ( 2997) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8328 (mp10) REVERT: A 56 MET cc_start: 0.7589 (ppp) cc_final: 0.7387 (ppp) REVERT: A 112 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8714 (pp30) REVERT: A 203 GLN cc_start: 0.8256 (tp40) cc_final: 0.7987 (tp40) REVERT: B 21 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8821 (mp10) REVERT: B 56 MET cc_start: 0.8053 (ppp) cc_final: 0.7780 (ppp) REVERT: B 112 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8706 (pp30) REVERT: B 203 GLN cc_start: 0.8439 (tp40) cc_final: 0.7891 (tm-30) REVERT: B 212 GLU cc_start: 0.7968 (tp30) cc_final: 0.7571 (tp30) REVERT: B 278 LYS cc_start: 0.8415 (ptmt) cc_final: 0.7877 (pttt) REVERT: C 56 MET cc_start: 0.8066 (ppp) cc_final: 0.7775 (ppp) REVERT: C 92 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8048 (tt0) REVERT: C 203 GLN cc_start: 0.8368 (tp40) cc_final: 0.8095 (tp40) REVERT: D 1 MET cc_start: 0.6457 (tpt) cc_final: 0.6041 (tpt) REVERT: D 56 MET cc_start: 0.8089 (ppp) cc_final: 0.7830 (ppp) REVERT: D 92 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8122 (tt0) REVERT: D 112 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8875 (tm-30) REVERT: D 202 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8423 (mtpt) REVERT: D 203 GLN cc_start: 0.8390 (tp40) cc_final: 0.8049 (tm-30) REVERT: D 278 LYS cc_start: 0.8016 (ptmt) cc_final: 0.7312 (ptpt) REVERT: E 56 MET cc_start: 0.8112 (ppp) cc_final: 0.7797 (ppp) REVERT: E 75 TYR cc_start: 0.7986 (m-10) cc_final: 0.7755 (m-10) REVERT: E 92 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8218 (tt0) REVERT: E 112 GLN cc_start: 0.9027 (pp30) cc_final: 0.8761 (pp30) REVERT: F 56 MET cc_start: 0.8085 (ppp) cc_final: 0.7801 (ppp) REVERT: F 134 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: F 203 GLN cc_start: 0.8317 (tp40) cc_final: 0.7915 (tm-30) REVERT: G 1 MET cc_start: 0.6289 (tpt) cc_final: 0.6034 (tpt) REVERT: G 21 GLN cc_start: 0.9171 (mt0) cc_final: 0.8496 (mp10) REVERT: G 112 GLN cc_start: 0.9112 (pp30) cc_final: 0.8688 (pp30) REVERT: G 203 GLN cc_start: 0.8396 (tp40) cc_final: 0.8176 (tp40) REVERT: G 255 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8389 (tm-30) outliers start: 31 outliers final: 18 residues processed: 198 average time/residue: 0.1301 time to fit residues: 37.7789 Evaluate side-chains 202 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 185 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN E 21 GLN E 203 GLN F 21 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.066467 restraints weight = 32674.850| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.65 r_work: 0.2903 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.215 15554 Z= 0.164 Angle : 0.759 59.193 20993 Z= 0.441 Chirality : 0.043 0.550 2520 Planarity : 0.003 0.027 2625 Dihedral : 9.666 59.938 2471 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.70 % Allowed : 15.17 % Favored : 83.13 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 1946 helix: 1.95 (0.16), residues: 1071 sheet: 0.64 (0.33), residues: 273 loop : -1.19 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 279 TYR 0.008 0.001 TYR D 250 PHE 0.007 0.001 PHE B 277 TRP 0.003 0.000 TRP G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (15554) covalent geometry : angle 0.75882 / 0.44 (20993) hydrogen bonds : bond 0.03927 / 2.67 ( 1020) hydrogen bonds : angle 4.02050 / 2.87 ( 2997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3773.66 seconds wall clock time: 65 minutes 13.13 seconds (3913.13 seconds total)