Starting phenix.real_space_refine on Sun Aug 24 01:40:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbd_37421/08_2025/8wbd_37421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbd_37421/08_2025/8wbd_37421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wbd_37421/08_2025/8wbd_37421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbd_37421/08_2025/8wbd_37421_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wbd_37421/08_2025/8wbd_37421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbd_37421/08_2025/8wbd_37421.map" } resolution = 2.9 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= 0.003 sd= 0.170 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 10218 2.51 5 N 2769 2.21 5 O 3044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 16157 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2596 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Chain: "a" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "b" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "c" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Chain: "b" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'TGL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.33, per 1000 atoms: 0.27 Number of scatterers: 16157 At special positions: 0 Unit cell: (124.1, 126.65, 120.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3044 8.00 N 2769 7.00 C 10218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 15 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 223 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 316 " distance=2.04 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS c 4 " - pdb=" SG CYS c 15 " distance=2.03 Simple disulfide: pdb=" SG CYS c 55 " - pdb=" SG CYS c 143 " distance=2.03 Simple disulfide: pdb=" SG CYS c 179 " - pdb=" SG CYS c 223 " distance=2.03 Simple disulfide: pdb=" SG CYS c 280 " - pdb=" SG CYS c 329 " distance=2.03 Simple disulfide: pdb=" SG CYS c 313 " - pdb=" SG CYS c 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 805.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 25 sheets defined 17.6% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.550A pdb=" N GLY A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.575A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.566A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.736A pdb=" N LEU A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.701A pdb=" N ASP B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 77 removed outlier: 3.786A pdb=" N ASN B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.629A pdb=" N LEU B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.632A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.523A pdb=" N ALA B 248 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.516A pdb=" N LEU B 270 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'C' and resid 40 through 53 removed outlier: 4.256A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 82 removed outlier: 3.689A pdb=" N ASN C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU C 74 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.670A pdb=" N THR C 230 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 271 removed outlier: 3.622A pdb=" N LEU C 270 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 271 " --> pdb=" O TRP C 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 267 through 271' Processing helix chain 'a' and resid 38 through 53 Processing helix chain 'a' and resid 61 through 82 removed outlier: 3.565A pdb=" N ASN a 65 " --> pdb=" O THR a 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE a 66 " --> pdb=" O ARG a 62 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET a 67 " --> pdb=" O LEU a 63 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN a 73 " --> pdb=" O LYS a 69 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU a 74 " --> pdb=" O GLN a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.698A pdb=" N LEU a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.635A pdb=" N THR a 230 " --> pdb=" O LYS a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.637A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.770A pdb=" N LEU a 270 " --> pdb=" O PRO a 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY a 271 " --> pdb=" O TRP a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 267 through 271' Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.738A pdb=" N MET a 345 " --> pdb=" O GLU a 342 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 51 Processing helix chain 'b' and resid 61 through 72 removed outlier: 3.680A pdb=" N ASN b 65 " --> pdb=" O THR b 61 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE b 66 " --> pdb=" O ARG b 62 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET b 67 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 83 removed outlier: 3.567A pdb=" N GLY b 83 " --> pdb=" O LEU b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 148 removed outlier: 3.704A pdb=" N ARG b 148 " --> pdb=" O ASN b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 183 Processing helix chain 'b' and resid 226 through 230 removed outlier: 3.581A pdb=" N THR b 230 " --> pdb=" O LYS b 227 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 Processing helix chain 'c' and resid 38 through 53 removed outlier: 3.617A pdb=" N ALA c 43 " --> pdb=" O PRO c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 82 removed outlier: 3.937A pdb=" N ILE c 66 " --> pdb=" O ARG c 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET c 67 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASN c 73 " --> pdb=" O LYS c 69 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU c 74 " --> pdb=" O GLN c 70 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY c 82 " --> pdb=" O VAL c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 144 through 148 removed outlier: 3.539A pdb=" N ARG c 147 " --> pdb=" O PRO c 144 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG c 148 " --> pdb=" O ASN c 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 144 through 148' Processing helix chain 'c' and resid 180 through 183 removed outlier: 3.840A pdb=" N LEU c 183 " --> pdb=" O ASP c 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 180 through 183' Processing helix chain 'c' and resid 226 through 230 removed outlier: 3.693A pdb=" N THR c 230 " --> pdb=" O LYS c 227 " (cutoff:3.500A) Processing helix chain 'c' and resid 244 through 248 removed outlier: 3.614A pdb=" N ALA c 248 " --> pdb=" O LYS c 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 271 removed outlier: 3.829A pdb=" N LEU c 270 " --> pdb=" O PRO c 267 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY c 271 " --> pdb=" O TRP c 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 267 through 271' Processing helix chain 'c' and resid 341 through 345 removed outlier: 3.501A pdb=" N ASN c 344 " --> pdb=" O LYS c 341 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET c 345 " --> pdb=" O GLU c 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 341 through 345' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.222A pdb=" N LYS A 33 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N MET A 169 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN A 35 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE A 171 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 166 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR A 158 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 7.081A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.578A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE A 212 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 200 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER a 205 " --> pdb=" O ILE a 212 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE a 212 " --> pdb=" O SER a 205 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.031A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.582A pdb=" N GLN B 35 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N PHE B 171 " --> pdb=" O GLN B 35 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 removed outlier: 7.034A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 4.778A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B 203 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 215 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP B 201 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE b 212 " --> pdb=" O SER b 205 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N GLU b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE b 277 " --> pdb=" O GLU b 213 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU b 274 " --> pdb=" O LEU b 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.489A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 298 through 302 removed outlier: 5.584A pdb=" N VAL B 346 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 16 removed outlier: 3.554A pdb=" N THR C 2 " --> pdb=" O VAL c 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.747A pdb=" N ASN C 166 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR C 158 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP C 168 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 89 through 90 removed outlier: 6.098A pdb=" N VAL C 89 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 57 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 330 through 331 removed outlier: 4.547A pdb=" N PHE C 277 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N GLU C 213 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE C 212 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N SER C 205 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 214 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS c 214 " --> pdb=" O GLU c 203 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER c 205 " --> pdb=" O ILE c 212 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE c 212 " --> pdb=" O SER c 205 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU c 213 " --> pdb=" O PHE c 277 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE c 277 " --> pdb=" O GLU c 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 287 removed outlier: 6.202A pdb=" N THR C 286 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 33 through 35 removed outlier: 6.592A pdb=" N ASN a 166 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR a 158 " --> pdb=" O ASN a 166 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.910A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.101A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 32 through 35 removed outlier: 6.366A pdb=" N LYS b 33 " --> pdb=" O ILE b 167 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N MET b 169 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN b 35 " --> pdb=" O MET b 169 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N PHE b 171 " --> pdb=" O GLN b 35 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN b 166 " --> pdb=" O TYR b 158 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR b 158 " --> pdb=" O ASN b 166 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP b 168 " --> pdb=" O GLU b 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 87 through 90 removed outlier: 6.958A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL b 89 " --> pdb=" O ILE b 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 284 through 287 removed outlier: 6.241A pdb=" N THR b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N CYS b 313 " --> pdb=" O THR b 284 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 33 through 35 removed outlier: 6.952A pdb=" N TRP c 168 " --> pdb=" O GLU c 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 89 through 90 removed outlier: 6.366A pdb=" N VAL c 89 " --> pdb=" O ILE c 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 284 through 287 419 hydrogen bonds defined for protein. 1104 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: 2.06 Time building geometry restraints manager: 1.67 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: 2691 1.31 - 1.44: 4592 1.44 - 1.57: 9113 1.57 - 1.69: 0 1.69 - 1.82: 180 Bond restraints: 16576 Sorted by residual: bond pdb=" CA ASN b 207 " pdb=" C ASN b 207 " ideal model delta sigma weight residual 1.531 1.468 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.27e-02 6.20e+03 1.13e+01 bond pdb=" OG3 TGL b 401 " pdb=" CC1 TGL b 401 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" OG1 TGL b 401 " pdb=" CA1 TGL b 401 " ideal model delta sigma weight residual 1.332 1.397 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CB1 TGL b 401 " pdb=" OG2 TGL b 401 " ideal model delta sigma weight residual 1.335 1.399 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 16571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 22072 1.85 - 3.70: 332 3.70 - 5.55: 51 5.55 - 7.39: 9 7.39 - 9.24: 3 Bond angle restraints: 22467 Sorted by residual: angle pdb=" N VAL C 25 " pdb=" CA VAL C 25 " pdb=" C VAL C 25 " ideal model delta sigma weight residual 112.04 105.42 6.62 1.40e+00 5.10e-01 2.23e+01 angle pdb=" N PRO C 320 " pdb=" CA PRO C 320 " pdb=" C PRO C 320 " ideal model delta sigma weight residual 111.13 117.49 -6.36 1.49e+00 4.50e-01 1.82e+01 angle pdb=" N TYR B 158 " pdb=" CA TYR B 158 " pdb=" C TYR B 158 " ideal model delta sigma weight residual 109.69 114.96 -5.27 1.44e+00 4.82e-01 1.34e+01 angle pdb=" O LYS b 206 " pdb=" C LYS b 206 " pdb=" N ASN b 207 " ideal model delta sigma weight residual 123.29 118.98 4.31 1.18e+00 7.18e-01 1.33e+01 angle pdb=" N ASN b 207 " pdb=" CA ASN b 207 " pdb=" C ASN b 207 " ideal model delta sigma weight residual 108.18 100.84 7.34 2.01e+00 2.48e-01 1.33e+01 ... (remaining 22462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 8960 17.65 - 35.30: 732 35.30 - 52.95: 122 52.95 - 70.59: 37 70.59 - 88.24: 15 Dihedral angle restraints: 9866 sinusoidal: 4046 harmonic: 5820 Sorted by residual: dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 316 " pdb=" CB CYS A 316 " ideal model delta sinusoidal sigma weight residual 93.00 177.34 -84.34 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS a 55 " pdb=" SG CYS a 55 " pdb=" SG CYS a 143 " pdb=" CB CYS a 143 " ideal model delta sinusoidal sigma weight residual -86.00 -143.76 57.76 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CA TYR B 158 " pdb=" C TYR B 158 " pdb=" N GLY B 159 " pdb=" CA GLY B 159 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 9863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1853 0.047 - 0.093: 396 0.093 - 0.140: 134 0.140 - 0.186: 2 0.186 - 0.233: 2 Chirality restraints: 2387 Sorted by residual: chirality pdb=" CA VAL B 78 " pdb=" N VAL B 78 " pdb=" C VAL B 78 " pdb=" CB VAL B 78 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL B 78 " pdb=" CA VAL B 78 " pdb=" CG1 VAL B 78 " pdb=" CG2 VAL B 78 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA VAL C 25 " pdb=" N VAL C 25 " pdb=" C VAL C 25 " pdb=" CB VAL C 25 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 2384 not shown) Planarity restraints: 2865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS b 206 " -0.015 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C LYS b 206 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS b 206 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN b 207 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 280 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO C 281 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 281 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 281 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 24 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ASN C 24 " -0.029 2.00e-02 2.50e+03 pdb=" O ASN C 24 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 25 " 0.010 2.00e-02 2.50e+03 ... (remaining 2862 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1073 2.74 - 3.28: 14674 3.28 - 3.82: 24917 3.82 - 4.36: 32176 4.36 - 4.90: 56207 Nonbonded interactions: 129047 Sorted by model distance: nonbonded pdb=" OG1 THR A 283 " pdb=" OH TYR A 331 " model vdw 2.195 3.040 nonbonded pdb=" O ASP b 23 " pdb=" OG1 THR b 27 " model vdw 2.236 3.040 nonbonded pdb=" OG SER C 297 " pdb=" O TYR C 331 " model vdw 2.278 3.040 nonbonded pdb=" OG SER c 297 " pdb=" O TYR c 331 " model vdw 2.279 3.040 nonbonded pdb=" O CYS c 143 " pdb=" NH2 ARG c 148 " model vdw 2.279 3.120 ... (remaining 129042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 133 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'C' selection = (chain 'a' and (resid 1 through 107 or resid 133 through 352)) selection = (chain 'b' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'c' } 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.320 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.003 0.066 16606 Z= 0.144 Angle : 0.572 9.243 22527 Z= 0.312 Chirality : 0.042 0.233 2387 Planarity : 0.003 0.048 2865 Dihedral : 13.554 88.243 6038 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.23 % Allowed : 0.40 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.64 (0.18), residues: 2022 helix: 0.89 (0.39), residues: 218 sheet: -1.81 (0.24), residues: 501 loop : -1.14 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 148 TYR 0.009 0.001 TYR B 77 PHE 0.015 0.001 PHE B 160 TRP 0.009 0.001 TRP A 28 HIS 0.003 0.001 HIS C 26 Details of bonding type rmsd covalent geometry : bond 0.00254 (16576) covalent geometry : angle 0.57085 (22467) SS BOND : bond 0.00227 ( 30) SS BOND : angle 1.00745 ( 60) hydrogen bonds : bond 0.22463 ( 419) hydrogen bonds : angle 8.84090 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 331 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.6974 (m-90) cc_final: 0.6771 (m-90) REVERT: A 73 ASN cc_start: 0.7450 (m110) cc_final: 0.7241 (m-40) REVERT: A 136 ASP cc_start: 0.9059 (m-30) cc_final: 0.8749 (m-30) REVERT: A 154 GLU cc_start: 0.8845 (pt0) cc_final: 0.8639 (pt0) REVERT: A 240 GLN cc_start: 0.8740 (mm110) cc_final: 0.8454 (mm110) REVERT: A 288 GLN cc_start: 0.8295 (pt0) cc_final: 0.8047 (pt0) REVERT: A 307 LEU cc_start: 0.8182 (tt) cc_final: 0.7982 (tp) REVERT: A 344 ASN cc_start: 0.6334 (m-40) cc_final: 0.5528 (p0) REVERT: A 345 MET cc_start: 0.7951 (mtm) cc_final: 0.7688 (mtp) REVERT: A 347 LYS cc_start: 0.7935 (ptmt) cc_final: 0.7631 (pttp) REVERT: B 31 GLN cc_start: 0.7342 (mt0) cc_final: 0.6890 (tp-100) REVERT: B 62 ARG cc_start: 0.7580 (ptm-80) cc_final: 0.7342 (ttp-110) REVERT: B 168 TRP cc_start: 0.8129 (m100) cc_final: 0.7914 (m100) REVERT: B 216 SER cc_start: 0.9272 (t) cc_final: 0.8977 (m) REVERT: B 314 ARG cc_start: 0.6880 (ttm-80) cc_final: 0.6337 (ttm170) REVERT: C 7 SER cc_start: 0.8354 (t) cc_final: 0.7997 (m) REVERT: C 146 GLU cc_start: 0.6612 (mp0) cc_final: 0.6368 (mp0) REVERT: C 213 GLU cc_start: 0.7968 (tt0) cc_final: 0.7738 (tt0) REVERT: C 258 GLN cc_start: 0.7643 (tp40) cc_final: 0.7419 (tp40) REVERT: a 292 ASP cc_start: 0.7520 (p0) cc_final: 0.6865 (t70) REVERT: a 314 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7652 (ttm170) REVERT: b 274 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7171 (mt-10) REVERT: b 293 HIS cc_start: 0.7990 (p-80) cc_final: 0.7755 (p-80) REVERT: c 102 ARG cc_start: 0.6856 (mmt90) cc_final: 0.6222 (tpp80) REVERT: c 147 ARG cc_start: 0.7269 (ptt-90) cc_final: 0.7067 (ttp-170) REVERT: c 255 ASN cc_start: 0.8735 (t0) cc_final: 0.8523 (t0) REVERT: c 312 CYS cc_start: 0.7472 (p) cc_final: 0.7206 (p) outliers start: 4 outliers final: 1 residues processed: 334 average time/residue: 0.5396 time to fit residues: 198.2961 Evaluate side-chains 247 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.0030 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN B 76 ASN B 207 ASN C 166 ASN C 208 GLN C 263 GLN b 208 GLN b 288 GLN c 145 ASN c 207 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.188378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131195 restraints weight = 16290.467| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.25 r_work: 0.3293 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 16606 Z= 0.260 Angle : 0.657 9.192 22527 Z= 0.343 Chirality : 0.047 0.163 2387 Planarity : 0.004 0.055 2865 Dihedral : 7.618 104.896 2228 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.33 % Favored : 93.62 % Rotamer: Outliers : 2.52 % Allowed : 9.78 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.71 (0.18), residues: 2022 helix: 0.83 (0.38), residues: 221 sheet: -1.44 (0.24), residues: 514 loop : -1.39 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 148 TYR 0.018 0.002 TYR c 256 PHE 0.016 0.002 PHE a 251 TRP 0.015 0.002 TRP A 28 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00639 (16576) covalent geometry : angle 0.65024 (22467) SS BOND : bond 0.00306 ( 30) SS BOND : angle 1.97755 ( 60) hydrogen bonds : bond 0.05726 ( 419) hydrogen bonds : angle 6.24421 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7311 (m-90) cc_final: 0.6947 (m-90) REVERT: A 73 ASN cc_start: 0.7764 (m110) cc_final: 0.7526 (m-40) REVERT: A 208 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7564 (mt0) REVERT: A 240 GLN cc_start: 0.8795 (mm110) cc_final: 0.8583 (mm110) REVERT: A 288 GLN cc_start: 0.8453 (pt0) cc_final: 0.8248 (pt0) REVERT: A 340 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: A 347 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7603 (pttp) REVERT: B 31 GLN cc_start: 0.7636 (mt0) cc_final: 0.7003 (tp-100) REVERT: B 170 LYS cc_start: 0.8114 (pttp) cc_final: 0.7868 (ptmt) REVERT: B 279 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: B 314 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6446 (ttm170) REVERT: C 67 MET cc_start: 0.8107 (ttt) cc_final: 0.7888 (ttp) REVERT: C 146 GLU cc_start: 0.6844 (mp0) cc_final: 0.6587 (mp0) REVERT: C 213 GLU cc_start: 0.8254 (tt0) cc_final: 0.8012 (tt0) REVERT: a 51 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6750 (mt-10) REVERT: a 287 ILE cc_start: 0.8312 (mm) cc_final: 0.8090 (mm) REVERT: a 292 ASP cc_start: 0.7509 (p0) cc_final: 0.6844 (t70) REVERT: b 293 HIS cc_start: 0.8032 (p-80) cc_final: 0.7776 (p-80) REVERT: c 33 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7346 (pttp) REVERT: c 102 ARG cc_start: 0.6937 (mmt90) cc_final: 0.6572 (tpp80) REVERT: c 173 GLU cc_start: 0.8050 (pm20) cc_final: 0.7719 (mm-30) REVERT: c 294 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6101 (ttt180) REVERT: c 312 CYS cc_start: 0.7862 (p) cc_final: 0.7398 (p) outliers start: 44 outliers final: 24 residues processed: 264 average time/residue: 0.5881 time to fit residues: 170.8068 Evaluate side-chains 248 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 157 ASP Chi-restraints excluded: chain b residue 164 THR Chi-restraints excluded: chain c residue 62 ARG Chi-restraints excluded: chain c residue 284 THR Chi-restraints excluded: chain c residue 294 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 70 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN C 208 GLN c 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.187635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133442 restraints weight = 16489.167| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.08 r_work: 0.3315 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16606 Z= 0.223 Angle : 0.626 9.680 22527 Z= 0.325 Chirality : 0.045 0.142 2387 Planarity : 0.004 0.039 2865 Dihedral : 7.299 61.379 2225 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.43 % Favored : 93.52 % Rotamer: Outliers : 3.89 % Allowed : 12.18 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.73 (0.18), residues: 2022 helix: 0.80 (0.37), residues: 221 sheet: -1.37 (0.24), residues: 514 loop : -1.45 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 147 TYR 0.018 0.002 TYR c 256 PHE 0.015 0.002 PHE a 251 TRP 0.014 0.002 TRP c 28 HIS 0.005 0.001 HIS b 26 Details of bonding type rmsd covalent geometry : bond 0.00546 (16576) covalent geometry : angle 0.62180 (22467) SS BOND : bond 0.00284 ( 30) SS BOND : angle 1.56529 ( 60) hydrogen bonds : bond 0.04823 ( 419) hydrogen bonds : angle 5.74739 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 237 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7362 (m-90) cc_final: 0.6969 (m-90) REVERT: A 73 ASN cc_start: 0.7668 (m110) cc_final: 0.7439 (m-40) REVERT: A 208 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: A 324 LEU cc_start: 0.8497 (mm) cc_final: 0.8146 (mm) REVERT: A 343 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6676 (pp20) REVERT: A 347 LYS cc_start: 0.8040 (ptmt) cc_final: 0.7685 (pttp) REVERT: B 31 GLN cc_start: 0.7599 (mt0) cc_final: 0.6883 (tp-100) REVERT: B 157 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7454 (t0) REVERT: B 170 LYS cc_start: 0.8140 (pttp) cc_final: 0.7911 (ptmt) REVERT: B 208 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: B 238 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: B 279 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: B 314 ARG cc_start: 0.7024 (ttm-80) cc_final: 0.6348 (ttm170) REVERT: C 67 MET cc_start: 0.8155 (ttt) cc_final: 0.7899 (ttp) REVERT: C 146 GLU cc_start: 0.6867 (mp0) cc_final: 0.6637 (mp0) REVERT: C 213 GLU cc_start: 0.8188 (tt0) cc_final: 0.7903 (tt0) REVERT: a 41 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.6635 (mtm180) REVERT: a 51 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6858 (mt-10) REVERT: b 30 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6292 (tt0) REVERT: c 33 LYS cc_start: 0.7694 (ptpt) cc_final: 0.7260 (pttp) REVERT: c 102 ARG cc_start: 0.6889 (mmt90) cc_final: 0.6410 (tpp80) REVERT: c 154 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: c 156 GLU cc_start: 0.8061 (tt0) cc_final: 0.7541 (tm-30) REVERT: c 173 GLU cc_start: 0.8081 (pm20) cc_final: 0.7738 (mm-30) REVERT: c 294 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6179 (ttt180) REVERT: c 312 CYS cc_start: 0.7887 (p) cc_final: 0.7442 (p) outliers start: 68 outliers final: 26 residues processed: 270 average time/residue: 0.5635 time to fit residues: 168.2111 Evaluate side-chains 260 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 41 ARG Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 140 THR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 30 GLU Chi-restraints excluded: chain b residue 164 THR Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 284 THR Chi-restraints excluded: chain c residue 294 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 179 optimal weight: 0.0370 chunk 10 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN C 70 GLN C 208 GLN b 288 GLN c 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.176033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117374 restraints weight = 16598.255| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.16 r_work: 0.2948 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16606 Z= 0.097 Angle : 0.513 8.931 22527 Z= 0.268 Chirality : 0.042 0.130 2387 Planarity : 0.003 0.034 2865 Dihedral : 6.967 63.981 2225 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.61 % Rotamer: Outliers : 2.80 % Allowed : 14.58 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.43 (0.18), residues: 2022 helix: 1.18 (0.38), residues: 221 sheet: -1.20 (0.24), residues: 520 loop : -1.24 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.016 0.001 TYR c 256 PHE 0.016 0.001 PHE B 160 TRP 0.009 0.001 TRP A 28 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00222 (16576) covalent geometry : angle 0.51021 (22467) SS BOND : bond 0.00200 ( 30) SS BOND : angle 1.16936 ( 60) hydrogen bonds : bond 0.03169 ( 419) hydrogen bonds : angle 5.29913 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7246 (m-90) cc_final: 0.6908 (m-90) REVERT: A 73 ASN cc_start: 0.7616 (m110) cc_final: 0.7416 (m-40) REVERT: A 208 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: A 347 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7622 (pttp) REVERT: B 208 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: B 279 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: B 314 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6404 (ttm170) REVERT: C 67 MET cc_start: 0.7958 (ttt) cc_final: 0.7687 (ttp) REVERT: C 146 GLU cc_start: 0.6805 (mp0) cc_final: 0.6580 (mp0) REVERT: C 213 GLU cc_start: 0.8304 (tt0) cc_final: 0.8002 (tt0) REVERT: a 51 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6765 (mt-10) REVERT: a 287 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8035 (mm) REVERT: a 292 ASP cc_start: 0.7614 (p0) cc_final: 0.6690 (t70) REVERT: b 147 ARG cc_start: 0.7423 (ttp-110) cc_final: 0.6982 (ttp-110) REVERT: b 184 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8523 (mtt) REVERT: c 33 LYS cc_start: 0.7598 (ptpt) cc_final: 0.7120 (pttp) REVERT: c 102 ARG cc_start: 0.6693 (mmt90) cc_final: 0.6161 (tpp80) REVERT: c 156 GLU cc_start: 0.8021 (tt0) cc_final: 0.7501 (tm-30) REVERT: c 170 LYS cc_start: 0.7612 (pttt) cc_final: 0.7328 (pttp) REVERT: c 294 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.5894 (ttt180) REVERT: c 312 CYS cc_start: 0.7551 (p) cc_final: 0.7228 (p) outliers start: 49 outliers final: 17 residues processed: 252 average time/residue: 0.5555 time to fit residues: 154.2572 Evaluate side-chains 240 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 345 MET Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 71 ILE Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain c residue 294 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 148 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 258 GLN B 70 GLN C 70 GLN C 208 GLN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 HIS c 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.174263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111151 restraints weight = 16658.139| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.18 r_work: 0.2882 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 16606 Z= 0.423 Angle : 0.797 10.484 22527 Z= 0.412 Chirality : 0.052 0.163 2387 Planarity : 0.005 0.051 2865 Dihedral : 7.690 58.655 2225 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.81 % Favored : 92.14 % Rotamer: Outliers : 4.17 % Allowed : 14.41 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.06 (0.18), residues: 2022 helix: 0.53 (0.36), residues: 221 sheet: -1.63 (0.25), residues: 474 loop : -1.66 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 182 TYR 0.022 0.003 TYR A 247 PHE 0.022 0.003 PHE a 323 TRP 0.018 0.003 TRP c 28 HIS 0.009 0.002 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.01045 (16576) covalent geometry : angle 0.79092 (22467) SS BOND : bond 0.00459 ( 30) SS BOND : angle 2.00851 ( 60) hydrogen bonds : bond 0.06249 ( 419) hydrogen bonds : angle 5.85738 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 224 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7099 (m-90) cc_final: 0.6755 (m-90) REVERT: A 73 ASN cc_start: 0.7532 (m110) cc_final: 0.7289 (m-40) REVERT: A 208 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: A 238 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7908 (tt0) REVERT: A 347 LYS cc_start: 0.8044 (ptmt) cc_final: 0.7691 (pttp) REVERT: B 31 GLN cc_start: 0.7663 (mt0) cc_final: 0.6673 (tp-100) REVERT: B 62 ARG cc_start: 0.7582 (ptm-80) cc_final: 0.7341 (ttp-110) REVERT: B 170 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7842 (ptmt) REVERT: B 203 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 208 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: B 279 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: B 314 ARG cc_start: 0.6981 (ttm-80) cc_final: 0.6233 (ttm170) REVERT: C 146 GLU cc_start: 0.6734 (mp0) cc_final: 0.6470 (mp0) REVERT: C 157 ASP cc_start: 0.8558 (m-30) cc_final: 0.8288 (m-30) REVERT: C 213 GLU cc_start: 0.8181 (tt0) cc_final: 0.7939 (tt0) REVERT: a 51 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6911 (mt-10) REVERT: b 30 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6505 (tt0) REVERT: b 184 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8564 (mtt) REVERT: c 33 LYS cc_start: 0.7437 (ptpt) cc_final: 0.6836 (pttp) REVERT: c 102 ARG cc_start: 0.6762 (mmt90) cc_final: 0.6354 (tpp80) REVERT: c 148 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6191 (ttp-170) REVERT: c 156 GLU cc_start: 0.7931 (tt0) cc_final: 0.7382 (tm-30) REVERT: c 173 GLU cc_start: 0.8129 (pm20) cc_final: 0.7677 (mm-30) REVERT: c 294 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6031 (ttt180) REVERT: c 310 GLN cc_start: 0.5813 (mm-40) cc_final: 0.5559 (mm110) outliers start: 73 outliers final: 36 residues processed: 262 average time/residue: 0.5795 time to fit residues: 167.1903 Evaluate side-chains 258 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 140 THR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 30 GLU Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 157 ASP Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 284 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 264 THR Chi-restraints excluded: chain c residue 284 THR Chi-restraints excluded: chain c residue 294 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 103 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN C 70 GLN C 208 GLN C 263 GLN b 288 GLN c 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.176523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116091 restraints weight = 16535.363| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.31 r_work: 0.2922 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16606 Z= 0.127 Angle : 0.552 10.465 22527 Z= 0.287 Chirality : 0.042 0.131 2387 Planarity : 0.003 0.031 2865 Dihedral : 7.180 62.024 2225 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 2.80 % Allowed : 16.52 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.62 (0.18), residues: 2022 helix: 1.03 (0.37), residues: 221 sheet: -1.30 (0.24), residues: 514 loop : -1.40 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 147 TYR 0.020 0.001 TYR c 256 PHE 0.019 0.001 PHE B 160 TRP 0.011 0.001 TRP A 28 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00303 (16576) covalent geometry : angle 0.54886 (22467) SS BOND : bond 0.00247 ( 30) SS BOND : angle 1.33332 ( 60) hydrogen bonds : bond 0.03555 ( 419) hydrogen bonds : angle 5.32056 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7135 (m-90) cc_final: 0.6792 (m-90) REVERT: A 73 ASN cc_start: 0.7500 (m110) cc_final: 0.7282 (m-40) REVERT: A 184 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8442 (mtt) REVERT: A 208 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7530 (mt0) REVERT: A 347 LYS cc_start: 0.8032 (ptmt) cc_final: 0.7645 (pttp) REVERT: B 31 GLN cc_start: 0.7613 (mt0) cc_final: 0.6806 (tp-100) REVERT: B 208 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: B 279 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: B 314 ARG cc_start: 0.7007 (ttm-80) cc_final: 0.6297 (ttm170) REVERT: C 146 GLU cc_start: 0.6729 (mp0) cc_final: 0.6480 (mp0) REVERT: C 213 GLU cc_start: 0.8314 (tt0) cc_final: 0.8057 (tt0) REVERT: a 51 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6774 (mt-10) REVERT: a 287 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7982 (mm) REVERT: a 292 ASP cc_start: 0.7462 (p0) cc_final: 0.6709 (t70) REVERT: b 147 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6893 (ttp-110) REVERT: c 33 LYS cc_start: 0.7545 (ptpt) cc_final: 0.6914 (pttp) REVERT: c 102 ARG cc_start: 0.6783 (mmt90) cc_final: 0.6144 (tpp80) REVERT: c 154 GLU cc_start: 0.8127 (tt0) cc_final: 0.7204 (tt0) REVERT: c 156 GLU cc_start: 0.7925 (tt0) cc_final: 0.7404 (tm-30) REVERT: c 294 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6000 (ttt180) REVERT: c 312 CYS cc_start: 0.7597 (p) cc_final: 0.7179 (p) outliers start: 49 outliers final: 20 residues processed: 240 average time/residue: 0.6122 time to fit residues: 162.2102 Evaluate side-chains 239 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain c residue 294 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN C 208 GLN C 263 GLN c 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.175012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.111095 restraints weight = 16438.573| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.35 r_work: 0.2965 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16606 Z= 0.101 Angle : 0.512 10.702 22527 Z= 0.264 Chirality : 0.042 0.130 2387 Planarity : 0.003 0.031 2865 Dihedral : 6.900 64.595 2225 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 2.46 % Allowed : 17.61 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.45 (0.18), residues: 2022 helix: 1.35 (0.38), residues: 221 sheet: -1.36 (0.25), residues: 490 loop : -1.24 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.021 0.001 TYR c 256 PHE 0.019 0.001 PHE B 160 TRP 0.010 0.001 TRP A 28 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00237 (16576) covalent geometry : angle 0.50887 (22467) SS BOND : bond 0.00266 ( 30) SS BOND : angle 1.24221 ( 60) hydrogen bonds : bond 0.03002 ( 419) hydrogen bonds : angle 5.08842 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7105 (m-90) cc_final: 0.6792 (m-90) REVERT: A 73 ASN cc_start: 0.7437 (m110) cc_final: 0.7228 (m-40) REVERT: A 184 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8432 (mtt) REVERT: A 208 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: A 347 LYS cc_start: 0.7966 (ptmt) cc_final: 0.7564 (pttp) REVERT: B 208 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: B 276 ASP cc_start: 0.7830 (p0) cc_final: 0.7377 (t0) REVERT: B 279 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: B 314 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6301 (ttm170) REVERT: C 146 GLU cc_start: 0.6701 (mp0) cc_final: 0.6464 (mp0) REVERT: C 213 GLU cc_start: 0.8213 (tt0) cc_final: 0.7915 (tt0) REVERT: a 51 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6678 (mt-10) REVERT: a 292 ASP cc_start: 0.7348 (p0) cc_final: 0.6693 (t70) REVERT: b 147 ARG cc_start: 0.7246 (ttp-110) cc_final: 0.6768 (ttp-110) REVERT: b 288 GLN cc_start: 0.7052 (tp40) cc_final: 0.6419 (pt0) REVERT: c 33 LYS cc_start: 0.7514 (ptpt) cc_final: 0.7018 (pttp) REVERT: c 102 ARG cc_start: 0.6706 (mmt90) cc_final: 0.6070 (tpp80) REVERT: c 154 GLU cc_start: 0.8028 (tt0) cc_final: 0.6942 (tt0) REVERT: c 156 GLU cc_start: 0.7930 (tt0) cc_final: 0.7421 (tm-30) REVERT: c 173 GLU cc_start: 0.8117 (pm20) cc_final: 0.7679 (mm-30) REVERT: c 294 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.5995 (ttt180) REVERT: c 312 CYS cc_start: 0.7510 (p) cc_final: 0.7132 (p) outliers start: 43 outliers final: 19 residues processed: 250 average time/residue: 0.5606 time to fit residues: 155.5564 Evaluate side-chains 248 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 140 THR Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain c residue 294 ARG Chi-restraints excluded: chain c residue 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.6980 chunk 181 optimal weight: 0.4980 chunk 131 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.0000 chunk 99 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN B 310 GLN C 263 GLN c 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.177526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115790 restraints weight = 16631.216| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.51 r_work: 0.2988 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16606 Z= 0.081 Angle : 0.485 10.821 22527 Z= 0.251 Chirality : 0.041 0.128 2387 Planarity : 0.003 0.030 2865 Dihedral : 6.649 66.085 2225 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 1.77 % Allowed : 18.75 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.14 (0.19), residues: 2022 helix: 1.49 (0.38), residues: 224 sheet: -1.09 (0.23), residues: 549 loop : -1.01 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 147 TYR 0.020 0.001 TYR c 256 PHE 0.020 0.001 PHE B 160 TRP 0.010 0.001 TRP B 168 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00183 (16576) covalent geometry : angle 0.48167 (22467) SS BOND : bond 0.00178 ( 30) SS BOND : angle 1.18148 ( 60) hydrogen bonds : bond 0.02515 ( 419) hydrogen bonds : angle 4.88767 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7156 (m-90) cc_final: 0.6833 (m-90) REVERT: A 30 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8286 (tt0) REVERT: A 208 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: A 347 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7620 (pttp) REVERT: B 146 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6840 (mm-30) REVERT: B 208 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: B 279 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: B 314 ARG cc_start: 0.6943 (ttm-80) cc_final: 0.6161 (ttm170) REVERT: C 35 GLN cc_start: 0.7868 (tp40) cc_final: 0.7566 (mm110) REVERT: C 146 GLU cc_start: 0.6617 (mp0) cc_final: 0.6410 (mp0) REVERT: C 213 GLU cc_start: 0.8231 (tt0) cc_final: 0.7933 (tt0) REVERT: a 51 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6721 (mt-10) REVERT: a 292 ASP cc_start: 0.7385 (p0) cc_final: 0.6794 (t70) REVERT: b 147 ARG cc_start: 0.7406 (ttp-110) cc_final: 0.6931 (ttp-110) REVERT: c 33 LYS cc_start: 0.7537 (ptpt) cc_final: 0.7078 (pttp) REVERT: c 102 ARG cc_start: 0.6689 (mmt90) cc_final: 0.6044 (tpp80) REVERT: c 145 ASN cc_start: 0.6769 (m-40) cc_final: 0.6535 (m110) REVERT: c 154 GLU cc_start: 0.8098 (tt0) cc_final: 0.7063 (tt0) REVERT: c 156 GLU cc_start: 0.7903 (tt0) cc_final: 0.7377 (tm-30) REVERT: c 173 GLU cc_start: 0.8078 (pm20) cc_final: 0.7678 (mm-30) REVERT: c 255 ASN cc_start: 0.8691 (t0) cc_final: 0.8409 (t0) REVERT: c 294 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6096 (ttt180) REVERT: c 312 CYS cc_start: 0.7338 (p) cc_final: 0.7112 (p) outliers start: 31 outliers final: 14 residues processed: 249 average time/residue: 0.5382 time to fit residues: 148.4247 Evaluate side-chains 239 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain c residue 294 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 176 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 165 optimal weight: 0.0770 chunk 91 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 163 optimal weight: 0.0370 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 84 HIS B 70 GLN B 310 GLN C 70 GLN b 70 GLN c 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.174020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110303 restraints weight = 16532.344| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.59 r_work: 0.2935 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16606 Z= 0.146 Angle : 0.550 10.979 22527 Z= 0.283 Chirality : 0.043 0.136 2387 Planarity : 0.003 0.036 2865 Dihedral : 6.828 63.681 2225 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.61 % Rotamer: Outliers : 1.89 % Allowed : 18.47 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.28 (0.19), residues: 2022 helix: 1.45 (0.37), residues: 224 sheet: -1.20 (0.24), residues: 509 loop : -1.13 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 41 TYR 0.021 0.001 TYR c 256 PHE 0.017 0.001 PHE B 160 TRP 0.010 0.001 TRP A 28 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00354 (16576) covalent geometry : angle 0.54525 (22467) SS BOND : bond 0.00255 ( 30) SS BOND : angle 1.47165 ( 60) hydrogen bonds : bond 0.03473 ( 419) hydrogen bonds : angle 5.08107 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7175 (m-90) cc_final: 0.6839 (m-90) REVERT: A 30 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8255 (tt0) REVERT: A 208 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: A 347 LYS cc_start: 0.8027 (ptmt) cc_final: 0.7653 (pttp) REVERT: B 208 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: B 279 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: B 314 ARG cc_start: 0.6954 (ttm-80) cc_final: 0.6154 (ttm170) REVERT: C 146 GLU cc_start: 0.6616 (mp0) cc_final: 0.6410 (mp0) REVERT: C 213 GLU cc_start: 0.8259 (tt0) cc_final: 0.7990 (tt0) REVERT: a 51 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6836 (mt-10) REVERT: a 292 ASP cc_start: 0.7427 (p0) cc_final: 0.6861 (t70) REVERT: b 147 ARG cc_start: 0.7348 (ttp-110) cc_final: 0.6804 (ttp-110) REVERT: c 33 LYS cc_start: 0.7572 (ptpt) cc_final: 0.6965 (pttp) REVERT: c 102 ARG cc_start: 0.6784 (mmt90) cc_final: 0.6116 (tpp80) REVERT: c 156 GLU cc_start: 0.7911 (tt0) cc_final: 0.7391 (tm-30) REVERT: c 294 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6144 (ttt180) REVERT: c 312 CYS cc_start: 0.7633 (p) cc_final: 0.7209 (p) outliers start: 33 outliers final: 20 residues processed: 245 average time/residue: 0.5375 time to fit residues: 146.1985 Evaluate side-chains 243 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 140 THR Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 294 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 0.0000 chunk 63 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 84 HIS B 70 GLN B 310 GLN C 70 GLN C 263 GLN b 70 GLN c 207 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.173748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109419 restraints weight = 16515.242| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.48 r_work: 0.2955 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16606 Z= 0.134 Angle : 0.545 10.722 22527 Z= 0.281 Chirality : 0.043 0.136 2387 Planarity : 0.003 0.034 2865 Dihedral : 6.829 63.534 2225 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 1.60 % Allowed : 19.10 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.29 (0.18), residues: 2022 helix: 1.53 (0.37), residues: 221 sheet: -1.25 (0.24), residues: 515 loop : -1.13 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 41 TYR 0.026 0.001 TYR C 256 PHE 0.018 0.001 PHE B 160 TRP 0.009 0.001 TRP A 28 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00324 (16576) covalent geometry : angle 0.54026 (22467) SS BOND : bond 0.00257 ( 30) SS BOND : angle 1.46645 ( 60) hydrogen bonds : bond 0.03355 ( 419) hydrogen bonds : angle 5.07377 ( 1104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7087 (m-90) cc_final: 0.6773 (m-90) REVERT: A 208 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: A 347 LYS cc_start: 0.7988 (ptmt) cc_final: 0.7609 (pttp) REVERT: B 208 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: B 276 ASP cc_start: 0.7781 (p0) cc_final: 0.7354 (t0) REVERT: B 279 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: B 314 ARG cc_start: 0.6919 (ttm-80) cc_final: 0.6117 (ttm170) REVERT: C 146 GLU cc_start: 0.6579 (mp0) cc_final: 0.6375 (mp0) REVERT: C 213 GLU cc_start: 0.8219 (tt0) cc_final: 0.7943 (tt0) REVERT: a 51 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6745 (mt-10) REVERT: a 292 ASP cc_start: 0.7385 (p0) cc_final: 0.6914 (t70) REVERT: b 147 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.6851 (ttp-110) REVERT: c 33 LYS cc_start: 0.7474 (ptpt) cc_final: 0.6958 (pttp) REVERT: c 102 ARG cc_start: 0.6767 (mmt90) cc_final: 0.6088 (tpp80) REVERT: c 156 GLU cc_start: 0.7875 (tt0) cc_final: 0.7345 (tm-30) REVERT: c 173 GLU cc_start: 0.8055 (pm20) cc_final: 0.7617 (mm-30) REVERT: c 294 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6085 (ttt180) REVERT: c 312 CYS cc_start: 0.7555 (p) cc_final: 0.7171 (p) outliers start: 28 outliers final: 20 residues processed: 238 average time/residue: 0.5776 time to fit residues: 152.6378 Evaluate side-chains 244 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain a residue 29 THR Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 140 THR Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 294 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7351 > 50: distance: 135 - 245: 31.713 distance: 138 - 242: 33.369 distance: 165 - 190: 31.114 distance: 168 - 187: 29.581 distance: 183 - 187: 27.908 distance: 187 - 188: 13.887 distance: 188 - 189: 10.778 distance: 188 - 191: 38.307 distance: 189 - 190: 31.073 distance: 189 - 201: 38.949 distance: 191 - 192: 27.220 distance: 192 - 193: 11.059 distance: 192 - 194: 10.086 distance: 193 - 195: 22.204 distance: 194 - 196: 21.262 distance: 194 - 197: 5.892 distance: 195 - 196: 6.216 distance: 196 - 198: 18.384 distance: 197 - 199: 17.006 distance: 198 - 200: 9.579 distance: 199 - 200: 20.603 distance: 201 - 202: 39.583 distance: 202 - 203: 14.963 distance: 202 - 205: 17.061 distance: 203 - 204: 46.660 distance: 203 - 213: 41.068 distance: 205 - 206: 16.238 distance: 206 - 207: 22.309 distance: 206 - 208: 37.697 distance: 207 - 209: 16.372 distance: 208 - 210: 4.462 distance: 209 - 211: 35.013 distance: 210 - 211: 9.094 distance: 211 - 212: 27.787 distance: 213 - 214: 16.801 distance: 214 - 215: 28.384 distance: 215 - 216: 31.415 distance: 215 - 217: 49.966 distance: 218 - 219: 14.347 distance: 218 - 221: 5.486 distance: 219 - 220: 12.830 distance: 219 - 225: 7.514 distance: 221 - 222: 44.342 distance: 222 - 223: 46.071 distance: 223 - 224: 30.939 distance: 225 - 226: 15.190 distance: 226 - 227: 19.438 distance: 226 - 229: 28.900 distance: 227 - 228: 11.867 distance: 227 - 234: 32.609 distance: 229 - 230: 25.656 distance: 230 - 231: 10.335 distance: 231 - 232: 34.726 distance: 231 - 233: 15.481 distance: 234 - 235: 24.845 distance: 235 - 236: 12.515 distance: 235 - 238: 23.793 distance: 236 - 237: 17.652 distance: 236 - 242: 49.269 distance: 238 - 239: 13.628 distance: 238 - 240: 22.845 distance: 239 - 241: 35.275 distance: 242 - 243: 36.866 distance: 243 - 244: 28.147 distance: 243 - 246: 53.727 distance: 244 - 245: 14.284 distance: 244 - 253: 29.817 distance: 246 - 247: 39.906 distance: 247 - 248: 40.130 distance: 248 - 249: 25.319 distance: 249 - 250: 12.724 distance: 250 - 251: 18.484 distance: 250 - 252: 30.841 distance: 253 - 254: 38.966 distance: 253 - 259: 20.969 distance: 254 - 255: 25.740 distance: 254 - 257: 35.037 distance: 255 - 256: 25.045 distance: 255 - 260: 16.181 distance: 258 - 259: 44.474 distance: 260 - 261: 21.748 distance: 261 - 262: 5.556 distance: 261 - 264: 7.573 distance: 262 - 263: 3.646 distance: 262 - 268: 8.776 distance: 264 - 265: 12.153 distance: 265 - 266: 11.327 distance: 265 - 267: 7.932 distance: 268 - 269: 18.671 distance: 269 - 270: 12.935 distance: 269 - 272: 10.610 distance: 270 - 271: 23.000 distance: 270 - 274: 27.232 distance: 272 - 273: 23.380