Starting phenix.real_space_refine on Sat May 17 19:54:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbd_37421/05_2025/8wbd_37421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbd_37421/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbd_37421/05_2025/8wbd_37421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbd_37421/05_2025/8wbd_37421.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbd_37421/05_2025/8wbd_37421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbd_37421/05_2025/8wbd_37421_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.14, per 1000 atoms: 0.57 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: 3.47 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.85 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: 4.58 Time building geometry restraints manager: 4.11 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: 1.420 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: 0.650 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 34.280 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP A 28 HIS 0.003 0.001 HIS C 26 PHE 0.015 0.001 PHE B 160 TYR 0.009 0.001 TYR B 77 ARG 0.004 0.000 ARG b 148 Details of bonding type rmsd hydrogen bonds : bond 0.22463 ( 419) hydrogen bonds : angle 8.84090 ( 1104) SS BOND : bond 0.00227 ( 30) SS BOND : angle 1.00745 ( 60) covalent geometry : bond 0.00254 (16576) covalent geometry : angle 0.57085 (22467) *********************** 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 : 1.590 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: 1.2790 time to fit residues: 471.5890 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 : 1.662 ------------------------------------------------------------------------------- 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 170 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.191631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135728 restraints weight = 16340.851| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.27 r_work: 0.3327 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16606 Z= 0.158 Angle : 0.564 7.456 22527 Z= 0.296 Chirality : 0.043 0.149 2387 Planarity : 0.004 0.053 2865 Dihedral : 7.302 104.076 2228 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.17 % Allowed : 9.03 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.18), residues: 2022 helix: 1.05 (0.38), residues: 220 sheet: -1.53 (0.24), residues: 484 loop : -1.26 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 28 HIS 0.004 0.001 HIS b 26 PHE 0.013 0.002 PHE a 251 TYR 0.016 0.001 TYR c 256 ARG 0.004 0.000 ARG c 148 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 419) hydrogen bonds : angle 6.19207 ( 1104) SS BOND : bond 0.00189 ( 30) SS BOND : angle 1.60863 ( 60) covalent geometry : bond 0.00378 (16576) covalent geometry : angle 0.55822 (22467) *********************** 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 289 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7330 (m-90) cc_final: 0.6978 (m-90) REVERT: A 73 ASN cc_start: 0.7774 (m110) cc_final: 0.7565 (m-40) REVERT: A 208 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: A 240 GLN cc_start: 0.8790 (mm110) cc_final: 0.8561 (mm110) REVERT: A 314 ARG cc_start: 0.7768 (ttm170) cc_final: 0.7488 (ttp80) REVERT: A 343 GLU cc_start: 0.6785 (pp20) cc_final: 0.6504 (pp20) REVERT: A 347 LYS cc_start: 0.7914 (ptmt) cc_final: 0.7498 (pttp) REVERT: B 31 GLN cc_start: 0.7656 (mt0) cc_final: 0.7002 (tp-100) REVERT: B 154 GLU cc_start: 0.8322 (pt0) cc_final: 0.8100 (pt0) REVERT: B 170 LYS cc_start: 0.8092 (pttp) cc_final: 0.7830 (ptmt) REVERT: B 279 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: B 314 ARG cc_start: 0.7001 (ttm-80) cc_final: 0.6453 (ttm170) REVERT: C 146 GLU cc_start: 0.6807 (mp0) cc_final: 0.6546 (mp0) REVERT: C 213 GLU cc_start: 0.8273 (tt0) cc_final: 0.8031 (tt0) REVERT: a 51 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6602 (mt-10) REVERT: a 292 ASP cc_start: 0.7484 (p0) cc_final: 0.6884 (t70) REVERT: b 147 ARG cc_start: 0.7547 (ttp-110) cc_final: 0.7282 (ttp-110) REVERT: b 293 HIS cc_start: 0.7979 (p-80) cc_final: 0.7702 (p-80) REVERT: c 33 LYS cc_start: 0.7771 (ptpt) cc_final: 0.7394 (pttp) REVERT: c 102 ARG cc_start: 0.6887 (mmt90) cc_final: 0.6542 (tpp80) REVERT: c 173 GLU cc_start: 0.8051 (pm20) cc_final: 0.7716 (mm-30) REVERT: c 312 CYS cc_start: 0.7775 (p) cc_final: 0.7377 (p) outliers start: 38 outliers final: 20 residues processed: 266 average time/residue: 1.4204 time to fit residues: 415.3625 Evaluate side-chains 242 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 136 ASP 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 98 SER 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 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 71 ILE Chi-restraints excluded: chain c residue 62 ARG Chi-restraints excluded: chain c residue 284 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 107 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 179 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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 b 208 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 = 0.4141 r_free = 0.4141 target = 0.187606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131102 restraints weight = 16272.798| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.20 r_work: 0.3260 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16606 Z= 0.244 Angle : 0.644 9.068 22527 Z= 0.334 Chirality : 0.046 0.146 2387 Planarity : 0.004 0.039 2865 Dihedral : 7.313 61.067 2225 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.47 % Rotamer: Outliers : 3.37 % Allowed : 11.84 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.18), residues: 2022 helix: 0.85 (0.37), residues: 221 sheet: -1.50 (0.25), residues: 478 loop : -1.44 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 28 HIS 0.006 0.001 HIS B 254 PHE 0.016 0.002 PHE a 251 TYR 0.019 0.002 TYR B 256 ARG 0.004 0.001 ARG c 147 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 419) hydrogen bonds : angle 5.80187 ( 1104) SS BOND : bond 0.00286 ( 30) SS BOND : angle 1.56334 ( 60) covalent geometry : bond 0.00603 (16576) covalent geometry : angle 0.63961 (22467) *********************** 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 298 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 239 time to evaluate : 1.849 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7282 (m-90) cc_final: 0.6908 (m-90) REVERT: A 73 ASN cc_start: 0.7632 (m110) cc_final: 0.7405 (m-40) REVERT: A 208 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: A 324 LEU cc_start: 0.8457 (mm) cc_final: 0.8154 (mm) REVERT: A 347 LYS cc_start: 0.8071 (ptmt) cc_final: 0.7709 (pttp) REVERT: B 31 GLN cc_start: 0.7522 (mt0) cc_final: 0.7029 (tp-100) REVERT: B 170 LYS cc_start: 0.8146 (pttp) cc_final: 0.7936 (ptmt) REVERT: B 208 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6928 (mp10) REVERT: B 238 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8530 (mt-10) REVERT: B 279 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6611 (mp0) REVERT: B 314 ARG cc_start: 0.7029 (ttm-80) cc_final: 0.6422 (ttm170) REVERT: C 58 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.6053 (mmp-170) REVERT: C 146 GLU cc_start: 0.6797 (mp0) cc_final: 0.6562 (mp0) REVERT: C 213 GLU cc_start: 0.7987 (tt0) cc_final: 0.7728 (tt0) REVERT: a 41 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6551 (mtm180) REVERT: a 51 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6856 (mt-10) REVERT: b 147 ARG cc_start: 0.7501 (ttp-110) cc_final: 0.7064 (ttp-110) REVERT: c 33 LYS cc_start: 0.7690 (ptpt) cc_final: 0.7292 (pttp) REVERT: c 102 ARG cc_start: 0.6850 (mmt90) cc_final: 0.6381 (tpp80) REVERT: c 154 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: c 156 GLU cc_start: 0.7946 (tt0) cc_final: 0.7429 (tm-30) REVERT: c 173 GLU cc_start: 0.8082 (pm20) cc_final: 0.7766 (mm-30) REVERT: c 312 CYS cc_start: 0.7823 (p) cc_final: 0.7377 (p) outliers start: 59 outliers final: 26 residues processed: 267 average time/residue: 1.2526 time to fit residues: 371.0047 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 : 1.812 ------------------------------------------------------------------------------- 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 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 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 58 ARG Chi-restraints excluded: chain C residue 70 GLN 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 164 THR Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 157 ASP Chi-restraints excluded: chain b residue 164 THR Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 284 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 b 288 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 = 0.4166 r_free = 0.4166 target = 0.190256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134506 restraints weight = 16293.661| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.13 r_work: 0.3324 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16606 Z= 0.120 Angle : 0.529 9.572 22527 Z= 0.277 Chirality : 0.042 0.131 2387 Planarity : 0.003 0.035 2865 Dihedral : 7.027 63.073 2225 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 2.80 % Allowed : 13.89 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.18), residues: 2022 helix: 1.11 (0.37), residues: 221 sheet: -1.22 (0.24), residues: 514 loop : -1.28 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 28 HIS 0.003 0.001 HIS A 195 PHE 0.015 0.001 PHE B 160 TYR 0.017 0.001 TYR c 256 ARG 0.003 0.000 ARG c 294 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 419) hydrogen bonds : angle 5.37937 ( 1104) SS BOND : bond 0.00191 ( 30) SS BOND : angle 1.23818 ( 60) covalent geometry : bond 0.00284 (16576) covalent geometry : angle 0.52565 (22467) *********************** 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 287 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7355 (m-90) cc_final: 0.6956 (m-90) REVERT: A 73 ASN cc_start: 0.7750 (m110) cc_final: 0.7539 (m-40) REVERT: A 184 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8411 (mtp) REVERT: A 208 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: A 343 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6705 (pp20) REVERT: A 347 LYS cc_start: 0.8059 (ptmt) cc_final: 0.7683 (pttp) REVERT: B 157 ASP cc_start: 0.8344 (p0) cc_final: 0.7542 (t0) REVERT: B 170 LYS cc_start: 0.8172 (pttp) cc_final: 0.7954 (ptmt) REVERT: B 208 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7012 (mp10) REVERT: B 238 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8619 (mt-10) REVERT: B 279 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: B 314 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6508 (ttm170) REVERT: C 146 GLU cc_start: 0.6806 (mp0) cc_final: 0.6591 (mp0) REVERT: C 213 GLU cc_start: 0.8233 (tt0) cc_final: 0.7987 (tt0) REVERT: a 41 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7986 (mtp85) REVERT: a 51 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6852 (mt-10) REVERT: a 287 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8174 (mm) REVERT: a 292 ASP cc_start: 0.7748 (p0) cc_final: 0.6827 (t70) REVERT: b 147 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7443 (ttp-110) REVERT: b 184 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8569 (mtt) REVERT: c 33 LYS cc_start: 0.7711 (ptpt) cc_final: 0.7294 (pttp) REVERT: c 102 ARG cc_start: 0.6840 (mmt90) cc_final: 0.6329 (tpp80) REVERT: c 154 GLU cc_start: 0.8301 (tt0) cc_final: 0.7372 (tt0) REVERT: c 156 GLU cc_start: 0.8068 (tt0) cc_final: 0.7564 (tm-30) REVERT: c 312 CYS cc_start: 0.7657 (p) cc_final: 0.7353 (p) outliers start: 49 outliers final: 16 residues processed: 256 average time/residue: 1.2317 time to fit residues: 350.0516 Evaluate side-chains 251 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 343 GLU 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 238 GLU 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 162 MET Chi-restraints excluded: chain C residue 177 GLU 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 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 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 22 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 99 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 165 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.181247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.121343 restraints weight = 16708.246| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.24 r_work: 0.2979 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1855 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= 0.095 Angle : 0.490 9.720 22527 Z= 0.255 Chirality : 0.041 0.129 2387 Planarity : 0.003 0.033 2865 Dihedral : 6.806 64.748 2225 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.74 % Allowed : 14.47 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2022 helix: 1.36 (0.38), residues: 221 sheet: -1.32 (0.24), residues: 514 loop : -1.13 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.002 0.001 HIS A 181 PHE 0.016 0.001 PHE B 160 TYR 0.018 0.001 TYR c 256 ARG 0.002 0.000 ARG c 294 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 419) hydrogen bonds : angle 5.10329 ( 1104) SS BOND : bond 0.00166 ( 30) SS BOND : angle 1.07015 ( 60) covalent geometry : bond 0.00221 (16576) covalent geometry : angle 0.48766 (22467) *********************** 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 281 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7143 (m-90) cc_final: 0.6828 (m-90) REVERT: A 208 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: A 314 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7466 (ttm170) REVERT: A 347 LYS cc_start: 0.7953 (ptmt) cc_final: 0.7484 (pttp) REVERT: B 208 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6948 (mp10) REVERT: B 238 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: B 276 ASP cc_start: 0.7876 (p0) cc_final: 0.7354 (t0) REVERT: B 279 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: B 314 ARG cc_start: 0.6968 (ttm-80) cc_final: 0.6428 (ttm170) REVERT: C 146 GLU cc_start: 0.6691 (mp0) cc_final: 0.6466 (mp0) REVERT: C 213 GLU cc_start: 0.8263 (tt0) cc_final: 0.7957 (tt0) REVERT: a 41 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7732 (mtp85) REVERT: a 51 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6620 (mt-10) REVERT: a 287 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8080 (mm) REVERT: a 292 ASP cc_start: 0.7474 (p0) cc_final: 0.6631 (t70) REVERT: b 30 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6367 (tt0) REVERT: b 147 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.7166 (ttp-110) REVERT: c 33 LYS cc_start: 0.7478 (ptpt) cc_final: 0.7038 (pttp) REVERT: c 102 ARG cc_start: 0.6694 (mmt90) cc_final: 0.6079 (tpp80) REVERT: c 154 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: c 156 GLU cc_start: 0.7979 (tt0) cc_final: 0.7463 (tm-30) REVERT: c 255 ASN cc_start: 0.8752 (t0) cc_final: 0.8415 (t0) REVERT: c 312 CYS cc_start: 0.7408 (p) cc_final: 0.7119 (p) outliers start: 48 outliers final: 19 residues processed: 253 average time/residue: 1.2810 time to fit residues: 359.3852 Evaluate side-chains 250 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 208 GLN Chi-restraints excluded: chain B residue 238 GLU 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 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 41 ARG 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 287 ILE 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 71 ILE Chi-restraints excluded: chain c residue 154 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 160 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 73 ASN A 258 GLN B 70 GLN B 310 GLN C 70 GLN C 208 GLN c 145 ASN c 207 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.179952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.117376 restraints weight = 16472.104| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.54 r_work: 0.2927 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16606 Z= 0.158 Angle : 0.546 10.077 22527 Z= 0.283 Chirality : 0.043 0.137 2387 Planarity : 0.003 0.034 2865 Dihedral : 6.962 63.385 2225 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 3.20 % Allowed : 14.69 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2022 helix: 1.31 (0.37), residues: 221 sheet: -1.26 (0.24), residues: 504 loop : -1.21 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 330 HIS 0.004 0.001 HIS B 254 PHE 0.014 0.002 PHE B 160 TYR 0.020 0.001 TYR c 256 ARG 0.003 0.000 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 419) hydrogen bonds : angle 5.23090 ( 1104) SS BOND : bond 0.00221 ( 30) SS BOND : angle 1.20432 ( 60) covalent geometry : bond 0.00386 (16576) covalent geometry : angle 0.54365 (22467) *********************** 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 284 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7161 (m-90) cc_final: 0.6829 (m-90) REVERT: A 184 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8488 (mtt) REVERT: A 208 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: A 340 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6083 (tm-30) REVERT: A 347 LYS cc_start: 0.7960 (ptmt) cc_final: 0.7524 (pttp) REVERT: B 208 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: B 279 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: B 314 ARG cc_start: 0.6899 (ttm-80) cc_final: 0.6257 (ttm170) REVERT: C 146 GLU cc_start: 0.6689 (mp0) cc_final: 0.6447 (mp0) REVERT: C 213 GLU cc_start: 0.8331 (tt0) cc_final: 0.8030 (tt0) REVERT: a 41 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7659 (mtp85) REVERT: a 51 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6657 (mt-10) REVERT: a 287 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7985 (mm) REVERT: a 292 ASP cc_start: 0.7415 (p0) cc_final: 0.6742 (t70) REVERT: b 30 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6384 (tt0) REVERT: b 147 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.7155 (ttp-110) REVERT: c 33 LYS cc_start: 0.7435 (ptpt) cc_final: 0.6962 (pttp) REVERT: c 102 ARG cc_start: 0.6652 (mmt90) cc_final: 0.6028 (tpp80) REVERT: c 154 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: c 156 GLU cc_start: 0.7976 (tt0) cc_final: 0.7485 (tm-30) REVERT: c 312 CYS cc_start: 0.7619 (p) cc_final: 0.7172 (p) outliers start: 56 outliers final: 27 residues processed: 253 average time/residue: 1.2401 time to fit residues: 348.8443 Evaluate side-chains 252 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 A residue 340 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE 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 177 GLU 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 41 ARG 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 156 GLU Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 284 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 30 GLU Chi-restraints excluded: chain b residue 71 ILE Chi-restraints excluded: chain b residue 157 ASP Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 123 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 70 GLN B 310 GLN C 70 GLN C 263 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 = 0.3919 r_free = 0.3919 target = 0.176636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114299 restraints weight = 16477.636| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.35 r_work: 0.2874 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 16606 Z= 0.280 Angle : 0.668 10.838 22527 Z= 0.344 Chirality : 0.047 0.149 2387 Planarity : 0.004 0.035 2865 Dihedral : 7.367 60.637 2225 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.22 % Favored : 92.73 % Rotamer: Outliers : 3.37 % Allowed : 15.32 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.18), residues: 2022 helix: 1.02 (0.37), residues: 221 sheet: -1.41 (0.24), residues: 498 loop : -1.44 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 168 HIS 0.006 0.001 HIS B 254 PHE 0.017 0.002 PHE a 251 TYR 0.021 0.002 TYR c 256 ARG 0.004 0.001 ARG c 182 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 419) hydrogen bonds : angle 5.54063 ( 1104) SS BOND : bond 0.00328 ( 30) SS BOND : angle 1.50160 ( 60) covalent geometry : bond 0.00690 (16576) covalent geometry : angle 0.66450 (22467) *********************** 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 286 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7161 (m-90) cc_final: 0.6806 (m-90) REVERT: A 184 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8458 (mtt) REVERT: A 208 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: A 340 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6147 (tm-30) REVERT: A 347 LYS cc_start: 0.8078 (ptmt) cc_final: 0.7672 (pttp) REVERT: B 31 GLN cc_start: 0.7599 (mt0) cc_final: 0.6858 (tp-100) REVERT: B 208 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: B 279 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: B 314 ARG cc_start: 0.7002 (ttm-80) cc_final: 0.6275 (ttm170) REVERT: C 146 GLU cc_start: 0.6657 (mp0) cc_final: 0.6324 (mp0) REVERT: C 213 GLU cc_start: 0.8286 (tt0) cc_final: 0.8036 (tt0) REVERT: a 41 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6444 (mtm180) REVERT: a 51 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6792 (mt-10) REVERT: a 292 ASP cc_start: 0.7486 (p0) cc_final: 0.6857 (t70) REVERT: b 30 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: b 147 ARG cc_start: 0.7426 (ttp-110) cc_final: 0.7069 (ttp-110) REVERT: c 33 LYS cc_start: 0.7494 (ptpt) cc_final: 0.6921 (pttp) REVERT: c 102 ARG cc_start: 0.6719 (mmt90) cc_final: 0.6262 (tpp80) REVERT: c 156 GLU cc_start: 0.7987 (tt0) cc_final: 0.7493 (tm-30) REVERT: c 170 LYS cc_start: 0.7621 (pttt) cc_final: 0.7356 (pttp) REVERT: c 312 CYS cc_start: 0.7858 (p) cc_final: 0.7298 (p) outliers start: 59 outliers final: 33 residues processed: 255 average time/residue: 1.2229 time to fit residues: 346.2912 Evaluate side-chains 260 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 184 MET 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 A residue 340 GLU Chi-restraints excluded: chain A residue 350 VAL 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 99 LYS Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 264 THR 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 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 41 ARG 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 156 GLU 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 47 LEU Chi-restraints excluded: chain b residue 157 ASP 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 154 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 62 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 70 GLN C 263 GLN C 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 = 0.3943 r_free = 0.3943 target = 0.179170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119525 restraints weight = 16420.331| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.46 r_work: 0.2950 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2140 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= 0.114 Angle : 0.527 10.678 22527 Z= 0.272 Chirality : 0.042 0.131 2387 Planarity : 0.003 0.032 2865 Dihedral : 6.970 63.470 2225 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 2.34 % Allowed : 16.81 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), residues: 2022 helix: 1.33 (0.37), residues: 221 sheet: -1.18 (0.23), residues: 540 loop : -1.20 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.003 0.001 HIS A 195 PHE 0.018 0.001 PHE B 160 TYR 0.022 0.001 TYR c 256 ARG 0.002 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 419) hydrogen bonds : angle 5.14431 ( 1104) SS BOND : bond 0.00182 ( 30) SS BOND : angle 1.12502 ( 60) covalent geometry : bond 0.00274 (16576) covalent geometry : angle 0.52480 (22467) *********************** 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 267 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7104 (m-90) cc_final: 0.6780 (m-90) REVERT: A 184 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8410 (mtt) REVERT: A 208 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: A 347 LYS cc_start: 0.7998 (ptmt) cc_final: 0.7583 (pttp) REVERT: B 157 ASP cc_start: 0.8100 (p0) cc_final: 0.7707 (t70) REVERT: B 208 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7079 (mp10) REVERT: B 276 ASP cc_start: 0.7820 (p0) cc_final: 0.7382 (t0) REVERT: B 279 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: B 314 ARG cc_start: 0.6993 (ttm-80) cc_final: 0.6274 (ttm170) REVERT: C 146 GLU cc_start: 0.6662 (mp0) cc_final: 0.6308 (mp0) REVERT: C 213 GLU cc_start: 0.8281 (tt0) cc_final: 0.8009 (tt0) REVERT: a 51 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6765 (mt-10) REVERT: a 292 ASP cc_start: 0.7370 (p0) cc_final: 0.6789 (t70) REVERT: b 30 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6377 (tt0) REVERT: b 147 ARG cc_start: 0.7552 (ttp-110) cc_final: 0.7229 (ttp-110) REVERT: c 33 LYS cc_start: 0.7501 (ptpt) cc_final: 0.6998 (pttp) REVERT: c 102 ARG cc_start: 0.6752 (mmt90) cc_final: 0.6114 (tpp80) REVERT: c 154 GLU cc_start: 0.8115 (tt0) cc_final: 0.7044 (tt0) REVERT: c 156 GLU cc_start: 0.7937 (tt0) cc_final: 0.7425 (tm-30) REVERT: c 312 CYS cc_start: 0.7422 (p) cc_final: 0.7054 (p) outliers start: 41 outliers final: 23 residues processed: 244 average time/residue: 1.2079 time to fit residues: 327.8546 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 : 1.660 ------------------------------------------------------------------------------- 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 99 LYS 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 6 VAL Chi-restraints excluded: chain C residue 27 THR 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 140 THR Chi-restraints excluded: chain a residue 284 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 47 LEU Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 284 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 20 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 117 optimal weight: 0.3980 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- 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 263 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 = 0.3919 r_free = 0.3919 target = 0.176743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113181 restraints weight = 16429.161| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.25 r_work: 0.2926 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16606 Z= 0.205 Angle : 0.608 11.260 22527 Z= 0.312 Chirality : 0.045 0.140 2387 Planarity : 0.003 0.033 2865 Dihedral : 7.151 62.068 2225 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.43 % Favored : 93.52 % Rotamer: Outliers : 2.86 % Allowed : 16.98 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.18), residues: 2022 helix: 1.15 (0.36), residues: 224 sheet: -1.34 (0.24), residues: 498 loop : -1.34 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP c 28 HIS 0.005 0.001 HIS B 254 PHE 0.016 0.002 PHE B 160 TYR 0.021 0.002 TYR c 256 ARG 0.005 0.000 ARG a 41 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 419) hydrogen bonds : angle 5.34238 ( 1104) SS BOND : bond 0.00281 ( 30) SS BOND : angle 1.58538 ( 60) covalent geometry : bond 0.00504 (16576) covalent geometry : angle 0.60313 (22467) *********************** 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 276 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7118 (m-90) cc_final: 0.6780 (m-90) REVERT: A 184 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8454 (mtt) REVERT: A 208 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: A 340 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6211 (tm-30) REVERT: A 347 LYS cc_start: 0.8038 (ptmt) cc_final: 0.7621 (pttp) REVERT: B 157 ASP cc_start: 0.8144 (p0) cc_final: 0.7744 (t70) REVERT: B 203 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8538 (mt-10) REVERT: B 208 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: B 279 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: B 314 ARG cc_start: 0.7031 (ttm-80) cc_final: 0.6308 (ttm170) REVERT: C 146 GLU cc_start: 0.6678 (mp0) cc_final: 0.6330 (mp0) REVERT: C 213 GLU cc_start: 0.8253 (tt0) cc_final: 0.8001 (tt0) REVERT: a 51 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6792 (mt-10) REVERT: a 292 ASP cc_start: 0.7384 (p0) cc_final: 0.6751 (t70) REVERT: b 30 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6375 (tt0) REVERT: b 147 ARG cc_start: 0.7476 (ttp-110) cc_final: 0.7096 (ttp-110) REVERT: c 33 LYS cc_start: 0.7505 (ptpt) cc_final: 0.6909 (pttp) REVERT: c 102 ARG cc_start: 0.6763 (mmt90) cc_final: 0.6135 (tpp80) REVERT: c 154 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: c 156 GLU cc_start: 0.7930 (tt0) cc_final: 0.7430 (tm-30) REVERT: c 312 CYS cc_start: 0.7709 (p) cc_final: 0.7254 (p) outliers start: 50 outliers final: 29 residues processed: 248 average time/residue: 1.2410 time to fit residues: 341.3018 Evaluate side-chains 256 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 177 GLU 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 A residue 340 GLU 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 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 6 VAL Chi-restraints excluded: chain C residue 27 THR 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 140 THR Chi-restraints excluded: chain a residue 156 GLU 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 26 HIS Chi-restraints excluded: chain b residue 30 GLU Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 284 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 139 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 154 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 179 optimal weight: 0.0870 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 70 GLN C 70 GLN C 263 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 = 0.3891 r_free = 0.3891 target = 0.174726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113395 restraints weight = 16628.457| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.29 r_work: 0.2912 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16606 Z= 0.147 Angle : 0.566 11.238 22527 Z= 0.291 Chirality : 0.043 0.135 2387 Planarity : 0.003 0.032 2865 Dihedral : 7.036 62.466 2225 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 2.12 % Allowed : 17.84 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2022 helix: 1.26 (0.37), residues: 224 sheet: -1.33 (0.24), residues: 504 loop : -1.27 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 28 HIS 0.004 0.001 HIS A 84 PHE 0.018 0.001 PHE B 160 TYR 0.022 0.001 TYR c 256 ARG 0.005 0.000 ARG a 41 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 419) hydrogen bonds : angle 5.21599 ( 1104) SS BOND : bond 0.00226 ( 30) SS BOND : angle 1.41117 ( 60) covalent geometry : bond 0.00357 (16576) covalent geometry : angle 0.56216 (22467) ********************** 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 256 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7146 (m-90) cc_final: 0.6813 (m-90) REVERT: A 84 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.5993 (p90) REVERT: A 184 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8476 (mtt) REVERT: A 208 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: A 340 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6219 (tm-30) REVERT: A 347 LYS cc_start: 0.8037 (ptmt) cc_final: 0.7625 (pttp) REVERT: B 157 ASP cc_start: 0.8146 (p0) cc_final: 0.7788 (t70) REVERT: B 208 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7164 (mp10) REVERT: B 279 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: B 314 ARG cc_start: 0.7011 (ttm-80) cc_final: 0.6291 (ttm170) REVERT: C 146 GLU cc_start: 0.6604 (mp0) cc_final: 0.6246 (mp0) REVERT: C 213 GLU cc_start: 0.8337 (tt0) cc_final: 0.8083 (tt0) REVERT: a 51 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6814 (mt-10) REVERT: a 292 ASP cc_start: 0.7385 (p0) cc_final: 0.6881 (t70) REVERT: b 30 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6381 (tt0) REVERT: b 147 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7201 (ttp-110) REVERT: c 33 LYS cc_start: 0.7562 (ptpt) cc_final: 0.7046 (pttp) REVERT: c 102 ARG cc_start: 0.6738 (mmt90) cc_final: 0.6109 (tpp80) REVERT: c 156 GLU cc_start: 0.7945 (tt0) cc_final: 0.7442 (tm-30) REVERT: c 312 CYS cc_start: 0.7619 (p) cc_final: 0.7172 (p) outliers start: 37 outliers final: 26 residues processed: 235 average time/residue: 1.2814 time to fit residues: 335.0304 Evaluate side-chains 250 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS 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 A residue 340 GLU 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 6 VAL Chi-restraints excluded: chain C residue 27 THR 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 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 156 GLU 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 26 HIS Chi-restraints excluded: chain b residue 30 GLU Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 284 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 284 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 70 GLN C 70 GLN C 263 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 = 0.3897 r_free = 0.3897 target = 0.175320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113093 restraints weight = 16495.482| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.25 r_work: 0.2937 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2216 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= 0.132 Angle : 0.552 11.123 22527 Z= 0.284 Chirality : 0.043 0.134 2387 Planarity : 0.003 0.036 2865 Dihedral : 6.940 63.098 2225 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 2.06 % Allowed : 17.95 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2022 helix: 1.37 (0.37), residues: 224 sheet: -1.35 (0.24), residues: 490 loop : -1.20 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 28 HIS 0.003 0.001 HIS B 254 PHE 0.017 0.001 PHE B 160 TYR 0.021 0.001 TYR c 256 ARG 0.005 0.000 ARG a 41 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 419) hydrogen bonds : angle 5.14745 ( 1104) SS BOND : bond 0.00218 ( 30) SS BOND : angle 1.32599 ( 60) covalent geometry : bond 0.00320 (16576) covalent geometry : angle 0.54801 (22467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13544.28 seconds wall clock time: 233 minutes 41.47 seconds (14021.47 seconds total)