Starting phenix.real_space_refine on Sun Aug 24 00:22:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pwn_20508/08_2025/6pwn_20508.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pwn_20508/08_2025/6pwn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pwn_20508/08_2025/6pwn_20508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pwn_20508/08_2025/6pwn_20508.map" model { file = "/net/cci-nas-00/data/ceres_data/6pwn_20508/08_2025/6pwn_20508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pwn_20508/08_2025/6pwn_20508.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 4.24, per 1000 atoms: 0.28 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: 1.48 Conformation dependent library (CDL) restraints added in 813.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.50 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: 2.65 Time building geometry restraints manager: 1.90 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: 8329 16.00 - 32.00: 840 32.00 - 48.00: 183 48.00 - 64.00: 56 64.00 - 80.00: 35 Dihedral angle restraints: 9443 sinusoidal: 3836 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 9440 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: 0.04 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.780 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 14.815 80.003 5831 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 aren 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 covalent geometry : bond 0.00846 (15554) covalent geometry : angle 0.86159 (20993) hydrogen bonds : bond 0.15611 ( 1020) hydrogen bonds : angle 6.55075 ( 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 : 0.632 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: 0.7664 (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: 0.8179 (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: 0.8152 (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: 0.1379 time to fit residues: 46.3688 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 : 0.475 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.092858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.063738 restraints weight = 33157.442| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.84 r_work: 0.2815 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1392 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 : 0.581 7.095 20993 Z= 0.307 Chirality : 0.044 0.163 2520 Planarity : 0.004 0.027 2625 Dihedral : 12.310 77.339 2515 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.38 % Allowed : 10.64 % Favored : 87.98 % 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 aren not related in a simple way. whole: -0.69 (0.18), residues: 1946 helix: 0.59 (0.16), residues: 1064 sheet: -0.56 (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 A 185 TYR 0.009 0.001 TYR D 250 PHE 0.008 0.001 PHE C 277 TRP 0.010 0.001 TRP G 16 Details of bonding type rmsd covalent geometry : bond 0.00510 (15554) covalent geometry : angle 0.58116 (20993) hydrogen bonds : bond 0.04840 ( 1020) hydrogen bonds : angle 4.74004 ( 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 237 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.570 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: 0.7982 (mtm) cc_final: 0.7620 (mmp) REVERT: A 112 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8882 (tm-30) REVERT: A 255 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8514 (tm-30) REVERT: B 112 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8875 (tm-30) REVERT: B 203 GLN cc_start: 0.8430 (tp40) cc_final: 0.8122 (tm-30) REVERT: B 278 LYS cc_start: 0.8487 (ptmt) cc_final: 0.7871 (pttt) REVERT: C 21 GLN cc_start: 0.9333 (pt0) cc_final: 0.9097 (pt0) REVERT: C 202 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8441 (mtpp) REVERT: D 92 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8206 (tt0) REVERT: D 112 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8949 (tm-30) REVERT: D 255 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8279 (tm-30) REVERT: D 278 LYS cc_start: 0.8266 (ptmt) cc_final: 0.7629 (ptpt) REVERT: E 75 TYR cc_start: 0.8285 (m-10) cc_final: 0.8060 (m-80) REVERT: E 278 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7619 (ptpt) REVERT: F 112 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8894 (tm-30) REVERT: F 203 GLN cc_start: 0.8322 (tp40) cc_final: 0.7757 (tm-30) REVERT: G 20 ASN cc_start: 0.8956 (t0) cc_final: 0.8741 (t0) REVERT: G 47 MET cc_start: 0.7088 (mmp) cc_final: 0.6870 (mmp) REVERT: G 92 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8060 (tt0) REVERT: G 255 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: G 278 LYS cc_start: 0.8247 (ptmt) cc_final: 0.7910 (ptpt) outliers start: 22 outliers final: 14 residues processed: 222 average time/residue: 0.1168 time to fit residues: 36.9855 Evaluate side-chains 196 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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: 0.9980 chunk 191 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065892 restraints weight = 33137.312| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.88 r_work: 0.2857 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1873 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= 0.119 Angle : 0.493 5.089 20993 Z= 0.262 Chirality : 0.042 0.161 2520 Planarity : 0.003 0.020 2625 Dihedral : 11.332 69.767 2513 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.45 % Allowed : 11.01 % Favored : 86.53 % 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 aren not related in a simple way. whole: 0.30 (0.19), residues: 1946 helix: 1.38 (0.16), residues: 1050 sheet: 0.06 (0.34), residues: 273 loop : -1.82 (0.21), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.005 0.001 TYR E 250 PHE 0.008 0.001 PHE A 277 TRP 0.019 0.001 TRP B 16 Details of bonding type rmsd covalent geometry : bond 0.00249 (15554) covalent geometry : angle 0.49266 (20993) hydrogen bonds : bond 0.03980 ( 1020) hydrogen bonds : angle 4.22155 ( 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 275 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.350 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: 0.6369 (tpt) cc_final: 0.6077 (tpt) REVERT: A 203 GLN cc_start: 0.8263 (tp40) cc_final: 0.8036 (tp40) REVERT: B 203 GLN cc_start: 0.8383 (tp40) cc_final: 0.8125 (tm-30) REVERT: B 212 GLU cc_start: 0.7835 (tp30) cc_final: 0.7503 (tp30) REVERT: B 278 LYS cc_start: 0.8473 (ptmt) cc_final: 0.7789 (pttt) REVERT: C 1 MET cc_start: 0.6448 (mmm) cc_final: 0.6215 (tpp) REVERT: C 97 ILE cc_start: 0.8890 (pt) cc_final: 0.8639 (mt) REVERT: D 1 MET cc_start: 0.6227 (mmm) cc_final: 0.5947 (tpp) REVERT: D 92 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8128 (tt0) REVERT: D 112 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8881 (tm-30) REVERT: D 203 GLN cc_start: 0.8338 (tp40) cc_final: 0.7849 (tm-30) REVERT: D 212 GLU cc_start: 0.7848 (tp30) cc_final: 0.7522 (tp30) REVERT: D 255 GLU cc_start: 0.8483 (tt0) cc_final: 0.8248 (tm-30) REVERT: E 47 MET cc_start: 0.7233 (mmp) cc_final: 0.7010 (mmp) REVERT: E 75 TYR cc_start: 0.8198 (m-10) cc_final: 0.7948 (m-80) REVERT: E 97 ILE cc_start: 0.8876 (pt) cc_final: 0.8665 (mp) REVERT: F 203 GLN cc_start: 0.8289 (tp40) cc_final: 0.7778 (tm-30) REVERT: G 75 TYR cc_start: 0.8040 (m-10) cc_final: 0.7822 (m-10) REVERT: G 92 GLN cc_start: 0.8931 (mm-40) cc_final: 0.7998 (tt0) REVERT: G 112 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8887 (tm-30) REVERT: G 202 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8573 (mtpp) REVERT: G 255 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8419 (tm-30) outliers start: 39 outliers final: 18 residues processed: 254 average time/residue: 0.1132 time to fit residues: 41.6144 Evaluate side-chains 210 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 31 ILE 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 21 GLN 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 126 MET 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: 5.9990 chunk 43 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 164 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 21 GLN B 21 GLN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 ASN D 21 GLN E 11 ASN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 21 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.065469 restraints weight = 32730.812| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.66 r_work: 0.2882 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 15554 Z= 0.161 Angle : 0.514 7.202 20993 Z= 0.275 Chirality : 0.042 0.147 2520 Planarity : 0.003 0.022 2625 Dihedral : 11.106 67.838 2513 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.27 % Allowed : 12.59 % Favored : 85.15 % 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 aren not related in a simple way. whole: 0.60 (0.19), residues: 1946 helix: 1.54 (0.16), residues: 1050 sheet: 0.32 (0.33), residues: 273 loop : -1.56 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 279 TYR 0.011 0.001 TYR C 250 PHE 0.011 0.001 PHE G 127 TRP 0.016 0.001 TRP G 16 Details of bonding type rmsd covalent geometry : bond 0.00358 (15554) covalent geometry : angle 0.51358 (20993) hydrogen bonds : bond 0.04102 ( 1020) hydrogen bonds : angle 4.22877 ( 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 237 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.588 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 1 MET cc_start: 0.6330 (tpt) cc_final: 0.6127 (tpt) REVERT: A 203 GLN cc_start: 0.8183 (tp40) cc_final: 0.7946 (tp40) REVERT: B 1 MET cc_start: 0.6682 (tpt) cc_final: 0.6317 (tpt) REVERT: B 203 GLN cc_start: 0.8414 (tp40) cc_final: 0.8193 (tm-30) REVERT: B 212 GLU cc_start: 0.7816 (tp30) cc_final: 0.7559 (tp30) REVERT: D 92 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8133 (tt0) REVERT: D 112 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8892 (tm-30) REVERT: D 203 GLN cc_start: 0.8359 (tp40) cc_final: 0.7690 (tm-30) REVERT: E 75 TYR cc_start: 0.8200 (m-10) cc_final: 0.7949 (m-80) REVERT: E 169 LYS cc_start: 0.9285 (ttpp) cc_final: 0.9036 (ttpt) REVERT: F 203 GLN cc_start: 0.8288 (tp40) cc_final: 0.7876 (tm-30) REVERT: G 1 MET cc_start: 0.6255 (mmm) cc_final: 0.6045 (tpp) REVERT: G 75 TYR cc_start: 0.8058 (m-10) cc_final: 0.7844 (m-10) REVERT: G 92 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8011 (tt0) REVERT: G 112 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8921 (tm-30) REVERT: G 202 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8562 (mtpp) REVERT: G 255 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8419 (tm-30) outliers start: 36 outliers final: 19 residues processed: 219 average time/residue: 0.1276 time to fit residues: 40.1009 Evaluate side-chains 207 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 31 ILE 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 E residue 31 ILE Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 155 MET 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: 1.9990 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 11 ASN B 21 GLN C 11 ASN C 21 GLN D 21 GLN E 203 GLN F 11 ASN F 21 GLN G 21 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.094444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064764 restraints weight = 32840.230| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.67 r_work: 0.2868 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15554 Z= 0.199 Angle : 0.534 7.800 20993 Z= 0.284 Chirality : 0.042 0.143 2520 Planarity : 0.003 0.024 2625 Dihedral : 10.985 67.842 2513 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.71 % Allowed : 13.03 % Favored : 84.27 % 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 aren not related in a simple way. whole: 0.65 (0.19), residues: 1946 helix: 1.53 (0.16), residues: 1050 sheet: 0.37 (0.33), residues: 273 loop : -1.46 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 279 TYR 0.012 0.001 TYR C 250 PHE 0.007 0.001 PHE G 127 TRP 0.006 0.001 TRP G 16 Details of bonding type rmsd covalent geometry : bond 0.00448 (15554) covalent geometry : angle 0.53424 (20993) hydrogen bonds : bond 0.04284 ( 1020) hydrogen bonds : angle 4.26849 ( 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 228 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.559 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 21 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8959 (mt0) REVERT: A 203 GLN cc_start: 0.8271 (tp40) cc_final: 0.8021 (tp40) REVERT: B 1 MET cc_start: 0.6756 (tpt) cc_final: 0.6487 (tpt) REVERT: B 203 GLN cc_start: 0.8484 (tp40) cc_final: 0.8244 (tm-30) REVERT: C 1 MET cc_start: 0.6859 (tpt) cc_final: 0.6574 (tpt) REVERT: C 203 GLN cc_start: 0.8441 (tp40) cc_final: 0.8105 (tm-30) REVERT: D 1 MET cc_start: 0.6854 (tpt) cc_final: 0.6192 (tpt) REVERT: D 21 GLN cc_start: 0.9213 (mt0) cc_final: 0.8725 (mp10) REVERT: D 92 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8139 (tt0) REVERT: D 112 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8902 (tm-30) REVERT: D 203 GLN cc_start: 0.8417 (tp40) cc_final: 0.7951 (tm-30) REVERT: D 278 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7493 (ptpt) REVERT: E 21 GLN cc_start: 0.9209 (mt0) cc_final: 0.8451 (mp10) REVERT: E 75 TYR cc_start: 0.8204 (m-10) cc_final: 0.7956 (m-80) REVERT: E 92 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8114 (tt0) REVERT: E 169 LYS cc_start: 0.9330 (ttpp) cc_final: 0.9122 (ttpt) REVERT: F 203 GLN cc_start: 0.8285 (tp40) cc_final: 0.7879 (tm-30) REVERT: G 112 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8966 (tm-30) REVERT: G 202 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8572 (mtpp) REVERT: G 255 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8426 (tm-30) outliers start: 43 outliers final: 30 residues processed: 208 average time/residue: 0.1223 time to fit residues: 36.7349 Evaluate side-chains 209 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 31 ILE 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 A residue 202 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain D residue 4 LEU 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 183 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 126 MET 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 31 ILE Chi-restraints excluded: chain G residue 255 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 84 optimal weight: 50.0000 chunk 156 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN C 21 GLN E 203 GLN F 21 GLN G 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065694 restraints weight = 32668.485| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.68 r_work: 0.2886 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15554 Z= 0.145 Angle : 0.499 7.237 20993 Z= 0.266 Chirality : 0.041 0.158 2520 Planarity : 0.002 0.022 2625 Dihedral : 10.763 66.948 2513 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.52 % Allowed : 13.85 % Favored : 83.64 % 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 aren not related in a simple way. whole: 0.88 (0.19), residues: 1946 helix: 1.74 (0.16), residues: 1043 sheet: 0.50 (0.33), residues: 273 loop : -1.38 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 279 TYR 0.008 0.001 TYR C 250 PHE 0.007 0.001 PHE G 127 TRP 0.005 0.001 TRP A 16 Details of bonding type rmsd covalent geometry : bond 0.00317 (15554) covalent geometry : angle 0.49917 (20993) hydrogen bonds : bond 0.04015 ( 1020) hydrogen bonds : angle 4.09555 ( 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 239 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.445 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 203 GLN cc_start: 0.8221 (tp40) cc_final: 0.7999 (tp40) REVERT: B 1 MET cc_start: 0.6657 (tpt) cc_final: 0.6323 (tpt) REVERT: B 203 GLN cc_start: 0.8419 (tp40) cc_final: 0.8195 (tm-30) REVERT: B 278 LYS cc_start: 0.8451 (ptmt) cc_final: 0.7933 (pttt) REVERT: C 1 MET cc_start: 0.6858 (tpt) cc_final: 0.6040 (tpt) REVERT: C 92 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8051 (tt0) REVERT: C 169 LYS cc_start: 0.9406 (ttpp) cc_final: 0.9205 (ttpp) REVERT: D 1 MET cc_start: 0.6797 (tpt) cc_final: 0.6114 (tpt) REVERT: D 21 GLN cc_start: 0.9169 (mt0) cc_final: 0.8481 (mp10) REVERT: D 92 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8125 (tt0) REVERT: D 112 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8874 (tm-30) REVERT: D 203 GLN cc_start: 0.8373 (tp40) cc_final: 0.7686 (tm-30) REVERT: E 21 GLN cc_start: 0.9137 (mt0) cc_final: 0.8412 (mp10) REVERT: E 47 MET cc_start: 0.7384 (mmp) cc_final: 0.7137 (mmp) REVERT: E 75 TYR cc_start: 0.8171 (m-10) cc_final: 0.7930 (m-80) REVERT: E 92 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8141 (tt0) REVERT: E 169 LYS cc_start: 0.9323 (ttpp) cc_final: 0.9115 (ttpt) REVERT: F 203 GLN cc_start: 0.8299 (tp40) cc_final: 0.7930 (tm-30) REVERT: G 112 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8909 (tm-30) REVERT: G 255 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8366 (tm-30) outliers start: 40 outliers final: 28 residues processed: 220 average time/residue: 0.1166 time to fit residues: 37.5133 Evaluate side-chains 209 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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 31 ILE 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 155 MET Chi-restraints excluded: chain D residue 4 LEU 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 E residue 4 LEU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 126 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 0.0000 chunk 173 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN F 21 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.065647 restraints weight = 32724.042| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.70 r_work: 0.2886 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2409 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= 0.153 Angle : 0.500 7.137 20993 Z= 0.267 Chirality : 0.041 0.158 2520 Planarity : 0.003 0.022 2625 Dihedral : 10.624 65.923 2513 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.39 % Allowed : 14.47 % Favored : 83.13 % 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 aren not related in a simple way. whole: 0.89 (0.19), residues: 1946 helix: 1.66 (0.16), residues: 1071 sheet: 0.53 (0.33), residues: 273 loop : -1.35 (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 C 250 PHE 0.006 0.001 PHE G 127 TRP 0.005 0.001 TRP F 16 Details of bonding type rmsd covalent geometry : bond 0.00337 (15554) covalent geometry : angle 0.50045 (20993) hydrogen bonds : bond 0.04027 ( 1020) hydrogen bonds : angle 4.08960 ( 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 226 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.344 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 203 GLN cc_start: 0.8289 (tp40) cc_final: 0.8017 (tp40) REVERT: B 203 GLN cc_start: 0.8416 (tp40) cc_final: 0.7881 (tm-30) REVERT: B 278 LYS cc_start: 0.8442 (ptmt) cc_final: 0.7927 (pttt) REVERT: C 1 MET cc_start: 0.6800 (tpt) cc_final: 0.6541 (tpt) REVERT: D 1 MET cc_start: 0.6746 (tpt) cc_final: 0.5983 (tpt) REVERT: D 92 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8121 (tt0) REVERT: D 112 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8878 (tm-30) REVERT: D 203 GLN cc_start: 0.8390 (tp40) cc_final: 0.7701 (tm-30) REVERT: D 278 LYS cc_start: 0.8103 (ptmt) cc_final: 0.7411 (ptpt) REVERT: E 47 MET cc_start: 0.7421 (mmp) cc_final: 0.7208 (mmp) REVERT: E 75 TYR cc_start: 0.8139 (m-10) cc_final: 0.7896 (m-80) REVERT: E 92 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8091 (tt0) REVERT: F 203 GLN cc_start: 0.8298 (tp40) cc_final: 0.7934 (tm-30) REVERT: G 21 GLN cc_start: 0.9193 (pt0) cc_final: 0.8709 (mt0) REVERT: G 112 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8921 (tm-30) REVERT: G 203 GLN cc_start: 0.8318 (tp40) cc_final: 0.8109 (tp40) REVERT: G 255 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8379 (tm-30) outliers start: 38 outliers final: 23 residues processed: 207 average time/residue: 0.1036 time to fit residues: 31.1562 Evaluate side-chains 206 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 A residue 202 LYS Chi-restraints excluded: chain B residue 31 ILE 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 155 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 E residue 155 MET Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 4 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 139 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 133 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 78 optimal weight: 0.0470 chunk 33 optimal weight: 7.9990 chunk 149 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN D 21 GLN 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 = 0.3638 r_free = 0.3638 target = 0.097641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068045 restraints weight = 32868.912| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.72 r_work: 0.2930 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15554 Z= 0.097 Angle : 0.480 7.620 20993 Z= 0.252 Chirality : 0.041 0.182 2520 Planarity : 0.002 0.020 2625 Dihedral : 10.228 63.375 2513 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.33 % Allowed : 14.60 % 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 aren not related in a simple way. whole: 1.25 (0.19), residues: 1946 helix: 1.98 (0.16), residues: 1071 sheet: 0.62 (0.33), residues: 273 loop : -1.24 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 279 TYR 0.004 0.001 TYR E 27 PHE 0.007 0.001 PHE A 277 TRP 0.005 0.001 TRP F 16 Details of bonding type rmsd covalent geometry : bond 0.00195 (15554) covalent geometry : angle 0.47968 (20993) hydrogen bonds : bond 0.03590 ( 1020) hydrogen bonds : angle 3.81766 ( 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 240 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.555 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 21 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: A 112 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8678 (pp30) REVERT: A 203 GLN cc_start: 0.8158 (tp40) cc_final: 0.7923 (tm-30) REVERT: B 1 MET cc_start: 0.6196 (tpt) cc_final: 0.5882 (tpt) REVERT: B 203 GLN cc_start: 0.8374 (tp40) cc_final: 0.7858 (tm-30) REVERT: B 278 LYS cc_start: 0.8428 (ptmt) cc_final: 0.8190 (ptpp) REVERT: C 1 MET cc_start: 0.6371 (tpt) cc_final: 0.5900 (tpt) REVERT: C 75 TYR cc_start: 0.8036 (m-10) cc_final: 0.7829 (m-10) REVERT: C 92 GLN cc_start: 0.8981 (mm-40) cc_final: 0.7943 (tt0) REVERT: C 134 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: C 278 LYS cc_start: 0.8473 (ptpt) cc_final: 0.7922 (pttt) REVERT: D 1 MET cc_start: 0.6334 (tpt) cc_final: 0.5850 (tpt) REVERT: D 21 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: D 92 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8094 (tt0) REVERT: D 112 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8740 (tm-30) REVERT: D 203 GLN cc_start: 0.8306 (tp40) cc_final: 0.8004 (tm-30) REVERT: D 212 GLU cc_start: 0.7859 (tp30) cc_final: 0.7554 (tp30) REVERT: D 278 LYS cc_start: 0.8081 (ptmt) cc_final: 0.7494 (ptpt) REVERT: E 21 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: E 56 MET cc_start: 0.8179 (ppp) cc_final: 0.7923 (ppp) REVERT: E 68 PHE cc_start: 0.7980 (m-80) cc_final: 0.7717 (m-10) REVERT: E 75 TYR cc_start: 0.7990 (m-10) cc_final: 0.7736 (m-80) REVERT: E 92 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8199 (tt0) REVERT: F 21 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8692 (mp10) REVERT: F 56 MET cc_start: 0.8103 (ppp) cc_final: 0.7811 (ppp) REVERT: F 112 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8671 (pp30) REVERT: F 134 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: F 203 GLN cc_start: 0.8173 (tp40) cc_final: 0.7784 (tm-30) REVERT: G 56 MET cc_start: 0.8256 (ppp) cc_final: 0.7928 (ppp) REVERT: G 92 GLN cc_start: 0.8872 (mm-40) cc_final: 0.7976 (tt0) REVERT: G 112 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8782 (tm-30) REVERT: G 134 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: G 255 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8393 (tm-30) outliers start: 37 outliers final: 12 residues processed: 222 average time/residue: 0.1099 time to fit residues: 35.8487 Evaluate side-chains 208 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 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 E residue 21 GLN Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 134 GLU 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: 1.9990 chunk 156 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN C 21 GLN ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN E 203 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067227 restraints weight = 32707.820| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.65 r_work: 0.2912 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15554 Z= 0.129 Angle : 0.515 7.496 20993 Z= 0.270 Chirality : 0.042 0.176 2520 Planarity : 0.002 0.021 2625 Dihedral : 10.171 62.262 2513 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.83 % Allowed : 15.48 % Favored : 82.69 % 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 aren not related in a simple way. whole: 1.20 (0.19), residues: 1946 helix: 1.90 (0.16), residues: 1078 sheet: 0.62 (0.33), residues: 273 loop : -1.22 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 279 TYR 0.008 0.001 TYR D 250 PHE 0.014 0.001 PHE A 127 TRP 0.003 0.000 TRP F 16 Details of bonding type rmsd covalent geometry : bond 0.00280 (15554) covalent geometry : angle 0.51464 (20993) hydrogen bonds : bond 0.03798 ( 1020) hydrogen bonds : angle 3.93636 ( 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 217 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.525 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: 0.9159 (mt0) cc_final: 0.8425 (mp10) REVERT: A 112 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8700 (pp30) REVERT: A 203 GLN cc_start: 0.8221 (tp40) cc_final: 0.7999 (tm-30) REVERT: B 1 MET cc_start: 0.6139 (tpt) cc_final: 0.5799 (tpt) REVERT: B 56 MET cc_start: 0.7926 (ppp) cc_final: 0.7719 (ppp) REVERT: B 203 GLN cc_start: 0.8405 (tp40) cc_final: 0.7864 (tm-30) REVERT: B 212 GLU cc_start: 0.8098 (tp30) cc_final: 0.7095 (tm-30) REVERT: C 1 MET cc_start: 0.6309 (tpt) cc_final: 0.5812 (tpt) REVERT: C 75 TYR cc_start: 0.8041 (m-10) cc_final: 0.7833 (m-10) REVERT: C 92 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8020 (tt0) REVERT: C 203 GLN cc_start: 0.8404 (tp40) cc_final: 0.8199 (tp40) REVERT: C 278 LYS cc_start: 0.8460 (ptpt) cc_final: 0.7913 (ptpt) REVERT: D 1 MET cc_start: 0.6228 (tpt) cc_final: 0.5722 (tpt) REVERT: D 21 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8331 (mp10) REVERT: D 92 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8144 (tt0) REVERT: D 112 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8768 (tm-30) REVERT: D 203 GLN cc_start: 0.8381 (tp40) cc_final: 0.7697 (tm-30) REVERT: D 212 GLU cc_start: 0.7841 (tp30) cc_final: 0.7538 (tp30) REVERT: D 278 LYS cc_start: 0.8091 (ptmt) cc_final: 0.7419 (ptpt) REVERT: E 56 MET cc_start: 0.8146 (ppp) cc_final: 0.7839 (ppp) REVERT: E 68 PHE cc_start: 0.8010 (m-80) cc_final: 0.7738 (m-10) REVERT: E 75 TYR cc_start: 0.7984 (m-10) cc_final: 0.7750 (m-80) REVERT: E 92 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8315 (tt0) REVERT: F 56 MET cc_start: 0.8107 (ppp) cc_final: 0.7821 (ppp) REVERT: F 134 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: F 203 GLN cc_start: 0.8234 (tp40) cc_final: 0.7817 (tm-30) REVERT: G 1 MET cc_start: 0.6341 (tpt) cc_final: 0.6073 (tpt) REVERT: G 56 MET cc_start: 0.8197 (ppp) cc_final: 0.7873 (ppp) REVERT: G 112 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8824 (tm-30) REVERT: G 134 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: G 203 GLN cc_start: 0.8329 (tp40) cc_final: 0.8111 (tp40) REVERT: G 255 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8382 (tm-30) outliers start: 29 outliers final: 16 residues processed: 204 average time/residue: 0.1124 time to fit residues: 33.4093 Evaluate side-chains 203 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU 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 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 E residue 155 MET Chi-restraints excluded: chain F residue 134 GLU 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: 6.9990 chunk 40 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 0.0020 chunk 147 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** G 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 = 0.3621 r_free = 0.3621 target = 0.096627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.067019 restraints weight = 32877.267| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.69 r_work: 0.2907 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15554 Z= 0.131 Angle : 0.520 8.011 20993 Z= 0.273 Chirality : 0.042 0.191 2520 Planarity : 0.002 0.021 2625 Dihedral : 10.051 61.150 2513 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.57 % Allowed : 15.92 % Favored : 82.50 % 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 aren not related in a simple way. whole: 1.25 (0.19), residues: 1946 helix: 1.95 (0.16), residues: 1071 sheet: 0.57 (0.33), residues: 259 loop : -1.08 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 279 TYR 0.008 0.001 TYR D 250 PHE 0.011 0.001 PHE A 127 TRP 0.006 0.001 TRP F 16 Details of bonding type rmsd covalent geometry : bond 0.00283 (15554) covalent geometry : angle 0.51994 (20993) hydrogen bonds : bond 0.03857 ( 1020) hydrogen bonds : angle 3.98851 ( 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 207 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.398 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 21 GLN cc_start: 0.9164 (mt0) cc_final: 0.8321 (mp10) REVERT: A 112 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8724 (pp30) REVERT: A 203 GLN cc_start: 0.8255 (tp40) cc_final: 0.7993 (tp40) REVERT: B 1 MET cc_start: 0.6301 (tpt) cc_final: 0.5988 (tpt) REVERT: B 21 GLN cc_start: 0.9278 (mt0) cc_final: 0.8740 (mp10) REVERT: B 56 MET cc_start: 0.7929 (ppp) cc_final: 0.7728 (ppp) REVERT: B 203 GLN cc_start: 0.8408 (tp40) cc_final: 0.7863 (tm-30) REVERT: B 212 GLU cc_start: 0.8112 (tp30) cc_final: 0.7056 (tm-30) REVERT: B 278 LYS cc_start: 0.8452 (ptmt) cc_final: 0.8037 (pttt) REVERT: C 1 MET cc_start: 0.6320 (tpt) cc_final: 0.5796 (tpt) REVERT: C 21 GLN cc_start: 0.9258 (pt0) cc_final: 0.8749 (mp10) REVERT: C 92 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8026 (tt0) REVERT: C 134 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: C 278 LYS cc_start: 0.8448 (ptpt) cc_final: 0.7916 (ptpt) REVERT: D 1 MET cc_start: 0.6320 (tpt) cc_final: 0.5859 (tpt) REVERT: D 56 MET cc_start: 0.8083 (ppp) cc_final: 0.7837 (ppp) REVERT: D 92 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8064 (tt0) REVERT: D 112 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8836 (tm-30) REVERT: D 203 GLN cc_start: 0.8378 (tp40) cc_final: 0.7702 (tm-30) REVERT: D 278 LYS cc_start: 0.8063 (ptmt) cc_final: 0.7367 (ptpt) REVERT: E 56 MET cc_start: 0.8151 (ppp) cc_final: 0.7841 (ppp) REVERT: E 68 PHE cc_start: 0.7980 (m-80) cc_final: 0.7714 (m-10) REVERT: E 75 TYR cc_start: 0.7924 (m-10) cc_final: 0.7698 (m-10) REVERT: E 92 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8194 (tt0) REVERT: E 112 GLN cc_start: 0.9029 (pp30) cc_final: 0.8668 (pp30) REVERT: F 21 GLN cc_start: 0.9329 (mt0) cc_final: 0.8611 (mp10) REVERT: F 56 MET cc_start: 0.8155 (ppp) cc_final: 0.7863 (ppp) REVERT: F 203 GLN cc_start: 0.8249 (tp40) cc_final: 0.7823 (tm-30) REVERT: G 82 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9079 (mm) REVERT: G 112 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8837 (tm-30) REVERT: G 134 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: G 203 GLN cc_start: 0.8326 (tp40) cc_final: 0.8101 (tp40) REVERT: G 255 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8384 (tm-30) outliers start: 25 outliers final: 15 residues processed: 197 average time/residue: 0.1101 time to fit residues: 31.6970 Evaluate side-chains 199 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU 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 227 GLU 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 E residue 155 MET Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 82 LEU 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 115 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 185 optimal weight: 0.0000 chunk 93 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 E 21 GLN E 203 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.068307 restraints weight = 32520.827| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.67 r_work: 0.2939 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15554 Z= 0.103 Angle : 0.501 8.466 20993 Z= 0.262 Chirality : 0.041 0.193 2520 Planarity : 0.002 0.020 2625 Dihedral : 9.730 61.254 2513 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.32 % Allowed : 16.24 % Favored : 82.44 % 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 aren not related in a simple way. whole: 1.41 (0.20), residues: 1946 helix: 2.03 (0.16), residues: 1078 sheet: 0.62 (0.33), residues: 259 loop : -0.96 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 279 TYR 0.004 0.001 TYR G 27 PHE 0.010 0.001 PHE A 127 TRP 0.004 0.001 TRP C 251 Details of bonding type rmsd covalent geometry : bond 0.00212 (15554) covalent geometry : angle 0.50096 (20993) hydrogen bonds : bond 0.03633 ( 1020) hydrogen bonds : angle 3.84537 ( 2997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3233.33 seconds wall clock time: 55 minutes 59.04 seconds (3359.04 seconds total)