Starting phenix.real_space_refine on Thu Feb 5 17:41:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9osr_70808/02_2026/9osr_70808.cif Found real_map, /net/cci-nas-00/data/ceres_data/9osr_70808/02_2026/9osr_70808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9osr_70808/02_2026/9osr_70808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9osr_70808/02_2026/9osr_70808.map" model { file = "/net/cci-nas-00/data/ceres_data/9osr_70808/02_2026/9osr_70808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9osr_70808/02_2026/9osr_70808.cif" } resolution = 2.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 120 5.16 5 C 11712 2.51 5 N 3238 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18822 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2982 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 370} Chain: "B" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2982 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 370} Chain: "C" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2987 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 371} Chain: "D" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2987 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 371} Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "N" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "K" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 926 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 785 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 785 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 926 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "M" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 3.66, per 1000 atoms: 0.19 Number of scatterers: 18822 At special positions: 0 Unit cell: (137.54, 137.54, 98.394, 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 120 16.00 O 3752 8.00 N 3238 7.00 C 11712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 232 " distance=2.04 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 618.4 milliseconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4392 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 50 sheets defined 4.0% alpha, 44.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.723A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.619A pdb=" N SER A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 463 through 467 removed outlier: 3.859A pdb=" N MET A 467 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.737A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.666A pdb=" N SER B 145 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN B 146 " --> pdb=" O GLY B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.634A pdb=" N MET B 467 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.673A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.513A pdb=" N SER C 145 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 146 " --> pdb=" O GLY C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 146' Processing helix chain 'C' and resid 463 through 467 removed outlier: 3.606A pdb=" N MET C 467 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.634A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.631A pdb=" N SER D 145 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 146 " --> pdb=" O GLY D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'D' and resid 463 through 467 removed outlier: 3.677A pdb=" N MET D 467 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.731A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.567A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.852A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.782A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.765A pdb=" N GLU R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.729A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 103 removed outlier: 3.790A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.786A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.751A pdb=" N SER A 179 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 225 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 225 removed outlier: 7.517A pdb=" N THR A 252 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 254 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.185A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER A 372 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG A 400 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR A 376 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL A 396 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LYS A 378 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG A 394 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 103 removed outlier: 3.791A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.790A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS B 175 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET B 160 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLN B 173 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.707A pdb=" N SER B 179 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 201 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLY B 216 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 203 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE B 205 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.719A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.859A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS B 280 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 355 removed outlier: 4.430A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER B 372 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP B 399 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 378 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 103 removed outlier: 3.706A pdb=" N GLY C 96 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.809A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR C 157 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS C 175 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N MET C 160 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN C 173 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.622A pdb=" N SER C 179 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 201 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY C 216 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 203 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER C 214 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE C 205 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.827A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 223 through 224 removed outlier: 6.416A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 276 through 283 removed outlier: 4.904A pdb=" N CYS C 278 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS C 280 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.423A pdb=" N TRP C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 363 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER C 372 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG C 400 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR C 376 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL C 396 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LYS C 378 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG C 394 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 96 through 103 removed outlier: 3.946A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.856A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N CYS D 175 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N MET D 160 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLN D 173 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.695A pdb=" N SER D 179 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 213 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 231 through 233 removed outlier: 3.958A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 276 through 283 removed outlier: 4.944A pdb=" N CYS D 278 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS D 280 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.604A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER D 372 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP D 399 " --> pdb=" O SER D 372 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS D 378 " --> pdb=" O ASN D 393 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASN D 393 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.549A pdb=" N THR J 110 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.549A pdb=" N THR J 110 " --> pdb=" O GLU J 10 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.594A pdb=" N VAL H 5 " --> pdb=" O MET H 23 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 8.244A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER H 112 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LYS H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 8.244A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER H 112 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LYS H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.619A pdb=" N LEU N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.619A pdb=" N LEU N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 18 through 24 Processing sheet with id=AD9, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AE1, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.679A pdb=" N PHE K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AE3, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.405A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AE5, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE6, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.431A pdb=" N TRP R 35 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 9 through 13 Processing sheet with id=AE8, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AF1, first strand: chain 'I' and resid 58 through 59 removed outlier: 6.707A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 58 through 59 removed outlier: 6.707A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.536A pdb=" N LEU M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.536A pdb=" N LEU M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 19 through 24 635 hydrogen bonds defined for protein. 1632 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: 3.68 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6202 1.35 - 1.47: 4982 1.47 - 1.59: 7922 1.59 - 1.71: 0 1.71 - 1.84: 152 Bond restraints: 19258 Sorted by residual: bond pdb=" CG PRO K 41 " pdb=" CD PRO K 41 " ideal model delta sigma weight residual 1.503 1.414 0.089 3.40e-02 8.65e+02 6.78e+00 bond pdb=" N VAL K 111 " pdb=" CA VAL K 111 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 5.94e+00 bond pdb=" N GLY J 106 " pdb=" CA GLY J 106 " ideal model delta sigma weight residual 1.446 1.470 -0.024 1.02e-02 9.61e+03 5.70e+00 bond pdb=" N VAL K 109 " pdb=" CA VAL K 109 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.14e-02 7.69e+03 5.26e+00 bond pdb=" N SER K 112 " pdb=" CA SER K 112 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.89e+00 ... (remaining 19253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 25424 1.86 - 3.72: 628 3.72 - 5.58: 59 5.58 - 7.44: 14 7.44 - 9.30: 7 Bond angle restraints: 26132 Sorted by residual: angle pdb=" CA PRO K 41 " pdb=" N PRO K 41 " pdb=" CD PRO K 41 " ideal model delta sigma weight residual 112.00 102.78 9.22 1.40e+00 5.10e-01 4.34e+01 angle pdb=" CA GLY K 106 " pdb=" C GLY K 106 " pdb=" O GLY K 106 " ideal model delta sigma weight residual 122.45 117.84 4.61 7.20e-01 1.93e+00 4.09e+01 angle pdb=" N PRO K 41 " pdb=" CD PRO K 41 " pdb=" CG PRO K 41 " ideal model delta sigma weight residual 103.20 94.01 9.19 1.50e+00 4.44e-01 3.75e+01 angle pdb=" CA GLY J 106 " pdb=" C GLY J 106 " pdb=" O GLY J 106 " ideal model delta sigma weight residual 122.23 118.02 4.21 6.90e-01 2.10e+00 3.72e+01 angle pdb=" C ARG C 430 " pdb=" N LYS C 431 " pdb=" CA LYS C 431 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 ... (remaining 26127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10005 17.92 - 35.84: 1023 35.84 - 53.77: 274 53.77 - 71.69: 47 71.69 - 89.61: 27 Dihedral angle restraints: 11376 sinusoidal: 4408 harmonic: 6968 Sorted by residual: dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS B 337 " pdb=" CB CYS B 337 " ideal model delta sinusoidal sigma weight residual 93.00 143.69 -50.69 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS D 318 " pdb=" SG CYS D 318 " pdb=" SG CYS D 337 " pdb=" CB CYS D 337 " ideal model delta sinusoidal sigma weight residual 93.00 140.92 -47.92 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CB CYS C 92 " pdb=" SG CYS C 92 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual 93.00 45.21 47.79 1 1.00e+01 1.00e-02 3.15e+01 ... (remaining 11373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2313 0.060 - 0.120: 447 0.120 - 0.180: 42 0.180 - 0.239: 4 0.239 - 0.299: 2 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA VAL J 109 " pdb=" N VAL J 109 " pdb=" C VAL J 109 " pdb=" CB VAL J 109 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB VAL K 109 " pdb=" CA VAL K 109 " pdb=" CG1 VAL K 109 " pdb=" CG2 VAL K 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL K 111 " pdb=" CA VAL K 111 " pdb=" CG1 VAL K 111 " pdb=" CG2 VAL K 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2805 not shown) Planarity restraints: 3390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA K 40 " -0.063 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO K 41 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO K 41 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO K 41 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 309 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" CG ASP D 309 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP D 309 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP D 309 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 356 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C ASP D 356 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP D 356 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY D 357 " 0.015 2.00e-02 2.50e+03 ... (remaining 3387 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1694 2.75 - 3.28: 17203 3.28 - 3.82: 32464 3.82 - 4.36: 40664 4.36 - 4.90: 70495 Nonbonded interactions: 162520 Sorted by model distance: nonbonded pdb=" NZ LYS B 415 " pdb=" OG SER B 416 " model vdw 2.208 3.120 nonbonded pdb=" OG SER D 298 " pdb=" O GLU D 343 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP C 399 " pdb=" OG SER C 457 " model vdw 2.269 3.040 nonbonded pdb=" O VAL C 317 " pdb=" OG SER C 335 " model vdw 2.273 3.040 nonbonded pdb=" NH2 ARG A 224 " pdb=" O GLY A 244 " model vdw 2.281 3.120 ... (remaining 162515 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 83 through 468) selection = (chain 'D' and resid 83 through 468) } ncs_group { reference = (chain 'H' and resid 4 through 113) selection = chain 'I' selection = (chain 'J' and resid 4 through 113) selection = chain 'K' } ncs_group { reference = chain 'L' selection = (chain 'M' and resid 4 through 106A) selection = (chain 'N' and resid 4 through 106A) selection = chain 'R' } 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: 3.250 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.670 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.004 0.092 19298 Z= 0.181 Angle : 0.699 9.297 26212 Z= 0.410 Chirality : 0.048 0.299 2808 Planarity : 0.005 0.091 3390 Dihedral : 15.968 89.609 6864 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.29 % Allowed : 18.50 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2444 helix: -1.28 (0.97), residues: 24 sheet: 0.77 (0.18), residues: 892 loop : -1.33 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 400 TYR 0.023 0.002 TYR L 49 PHE 0.019 0.002 PHE D 410 TRP 0.015 0.001 TRP D 295 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00356 (19258) covalent geometry : angle 0.69749 (26132) SS BOND : bond 0.00315 ( 40) SS BOND : angle 0.99396 ( 80) hydrogen bonds : bond 0.10435 ( 590) hydrogen bonds : angle 6.91347 ( 1632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 399 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 318 CYS cc_start: 0.6826 (m) cc_final: 0.6574 (m) REVERT: L 36 TYR cc_start: 0.8852 (m-80) cc_final: 0.8579 (m-80) REVERT: R 36 TYR cc_start: 0.8962 (m-80) cc_final: 0.8666 (m-80) outliers start: 27 outliers final: 16 residues processed: 416 average time/residue: 0.5423 time to fit residues: 253.9608 Evaluate side-chains 405 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 389 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN C 93 ASN C 226 GLN C 441 ASN D 441 ASN L 79 GLN M 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.122971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.115733 restraints weight = 24423.273| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.03 r_work: 0.3653 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19298 Z= 0.219 Angle : 0.581 9.314 26212 Z= 0.313 Chirality : 0.047 0.176 2808 Planarity : 0.005 0.051 3390 Dihedral : 5.517 47.881 2698 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.82 % Allowed : 15.25 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2444 helix: -1.42 (0.98), residues: 24 sheet: 0.70 (0.18), residues: 886 loop : -1.32 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 152 TYR 0.023 0.002 TYR L 49 PHE 0.019 0.002 PHE C 422 TRP 0.014 0.002 TRP D 295 HIS 0.007 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00509 (19258) covalent geometry : angle 0.57783 (26132) SS BOND : bond 0.00357 ( 40) SS BOND : angle 1.17346 ( 80) hydrogen bonds : bond 0.03674 ( 590) hydrogen bonds : angle 5.75211 ( 1632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 405 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7255 (ttm-80) REVERT: D 318 CYS cc_start: 0.6856 (m) cc_final: 0.6407 (m) REVERT: J 80 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8027 (ttm) outliers start: 80 outliers final: 43 residues processed: 436 average time/residue: 0.5614 time to fit residues: 275.7321 Evaluate side-chains 437 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 392 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 86 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN C 93 ASN C 226 GLN C 441 ASN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100CASN M 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.123501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116249 restraints weight = 24524.859| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.04 r_work: 0.3656 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19298 Z= 0.183 Angle : 0.551 7.763 26212 Z= 0.297 Chirality : 0.046 0.172 2808 Planarity : 0.004 0.048 3390 Dihedral : 5.269 52.348 2687 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.73 % Allowed : 16.06 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2444 helix: -1.47 (0.97), residues: 24 sheet: 0.85 (0.17), residues: 880 loop : -1.27 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 83 TYR 0.022 0.001 TYR L 49 PHE 0.016 0.002 PHE C 422 TRP 0.013 0.001 TRP D 295 HIS 0.004 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00421 (19258) covalent geometry : angle 0.54821 (26132) SS BOND : bond 0.00333 ( 40) SS BOND : angle 1.21730 ( 80) hydrogen bonds : bond 0.03393 ( 590) hydrogen bonds : angle 5.54676 ( 1632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 393 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7367 (ttm-80) REVERT: C 230 CYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7453 (p) REVERT: D 318 CYS cc_start: 0.6758 (m) cc_final: 0.6461 (m) REVERT: K 91 TYR cc_start: 0.8494 (m-80) cc_final: 0.8086 (m-80) REVERT: L 36 TYR cc_start: 0.8587 (m-80) cc_final: 0.8335 (m-80) outliers start: 78 outliers final: 42 residues processed: 424 average time/residue: 0.6109 time to fit residues: 290.6769 Evaluate side-chains 432 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 388 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 181 optimal weight: 0.0370 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN C 93 ASN C 226 GLN D 91 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.123217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.115985 restraints weight = 24627.129| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.04 r_work: 0.3655 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19298 Z= 0.177 Angle : 0.544 7.498 26212 Z= 0.293 Chirality : 0.045 0.172 2808 Planarity : 0.004 0.045 3390 Dihedral : 5.198 56.444 2685 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.68 % Allowed : 16.16 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2444 helix: -1.41 (0.98), residues: 24 sheet: 0.87 (0.17), residues: 864 loop : -1.25 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 83 TYR 0.022 0.001 TYR L 49 PHE 0.016 0.002 PHE C 422 TRP 0.013 0.001 TRP B 178 HIS 0.004 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00409 (19258) covalent geometry : angle 0.54091 (26132) SS BOND : bond 0.00330 ( 40) SS BOND : angle 1.22485 ( 80) hydrogen bonds : bond 0.03318 ( 590) hydrogen bonds : angle 5.46961 ( 1632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 399 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7268 (ttm-80) REVERT: K 91 TYR cc_start: 0.8509 (m-80) cc_final: 0.8092 (m-80) outliers start: 77 outliers final: 52 residues processed: 428 average time/residue: 0.5688 time to fit residues: 273.7550 Evaluate side-chains 442 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 389 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 238 optimal weight: 0.4980 chunk 216 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN C 93 ASN C 226 GLN C 441 ASN D 91 GLN D 226 GLN H 100CASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.125209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.117523 restraints weight = 24013.856| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.13 r_work: 0.3651 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19298 Z= 0.168 Angle : 0.541 7.223 26212 Z= 0.291 Chirality : 0.045 0.172 2808 Planarity : 0.004 0.045 3390 Dihedral : 5.083 58.307 2683 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.44 % Allowed : 17.11 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2444 helix: -1.37 (0.98), residues: 24 sheet: 0.91 (0.18), residues: 864 loop : -1.25 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 400 TYR 0.022 0.001 TYR L 49 PHE 0.015 0.002 PHE C 354 TRP 0.013 0.001 TRP B 178 HIS 0.004 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00387 (19258) covalent geometry : angle 0.53845 (26132) SS BOND : bond 0.00303 ( 40) SS BOND : angle 1.13709 ( 80) hydrogen bonds : bond 0.03259 ( 590) hydrogen bonds : angle 5.38802 ( 1632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 399 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 230 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7526 (p) REVERT: B 292 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7374 (ttm-80) REVERT: K 91 TYR cc_start: 0.8607 (m-80) cc_final: 0.8146 (m-80) REVERT: L 36 TYR cc_start: 0.8703 (m-80) cc_final: 0.8429 (m-80) outliers start: 72 outliers final: 52 residues processed: 428 average time/residue: 0.5610 time to fit residues: 269.7709 Evaluate side-chains 449 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 395 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 93 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 226 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 347 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.123967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116270 restraints weight = 23839.223| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.12 r_work: 0.3637 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19298 Z= 0.219 Angle : 0.569 8.188 26212 Z= 0.306 Chirality : 0.047 0.173 2808 Planarity : 0.004 0.047 3390 Dihedral : 5.230 55.434 2683 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.68 % Allowed : 17.02 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2444 helix: -1.42 (0.97), residues: 24 sheet: 0.80 (0.17), residues: 894 loop : -1.26 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 400 TYR 0.029 0.002 TYR L 49 PHE 0.018 0.002 PHE C 422 TRP 0.014 0.002 TRP D 295 HIS 0.005 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00509 (19258) covalent geometry : angle 0.56566 (26132) SS BOND : bond 0.00351 ( 40) SS BOND : angle 1.29213 ( 80) hydrogen bonds : bond 0.03500 ( 590) hydrogen bonds : angle 5.48767 ( 1632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 392 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7468 (ttm-80) REVERT: D 318 CYS cc_start: 0.6857 (m) cc_final: 0.6567 (m) REVERT: K 91 TYR cc_start: 0.8622 (m-80) cc_final: 0.8178 (m-80) REVERT: L 36 TYR cc_start: 0.8703 (m-80) cc_final: 0.8436 (m-80) outliers start: 77 outliers final: 59 residues processed: 425 average time/residue: 0.5616 time to fit residues: 268.4802 Evaluate side-chains 446 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 386 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 189 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 226 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN H 100CASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.116344 restraints weight = 24047.624| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.13 r_work: 0.3639 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19298 Z= 0.207 Angle : 0.565 7.837 26212 Z= 0.304 Chirality : 0.046 0.173 2808 Planarity : 0.004 0.052 3390 Dihedral : 5.202 54.821 2683 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.63 % Allowed : 16.97 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2444 helix: -1.39 (0.99), residues: 24 sheet: 0.83 (0.18), residues: 880 loop : -1.28 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 400 TYR 0.026 0.002 TYR L 49 PHE 0.018 0.002 PHE C 422 TRP 0.014 0.002 TRP D 295 HIS 0.004 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00479 (19258) covalent geometry : angle 0.56175 (26132) SS BOND : bond 0.00342 ( 40) SS BOND : angle 1.28462 ( 80) hydrogen bonds : bond 0.03433 ( 590) hydrogen bonds : angle 5.46305 ( 1632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 389 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7406 (ttm-80) REVERT: D 318 CYS cc_start: 0.6873 (m) cc_final: 0.6557 (m) REVERT: K 91 TYR cc_start: 0.8620 (m-80) cc_final: 0.8182 (m-80) REVERT: R 36 TYR cc_start: 0.8744 (m-80) cc_final: 0.8484 (m-80) outliers start: 76 outliers final: 61 residues processed: 421 average time/residue: 0.5523 time to fit residues: 261.1452 Evaluate side-chains 448 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 386 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 205 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN A 441 ASN B 226 GLN C 93 ASN C 226 GLN C 441 ASN D 91 GLN H 100CASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116417 restraints weight = 23980.702| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.13 r_work: 0.3643 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19298 Z= 0.188 Angle : 0.556 7.632 26212 Z= 0.299 Chirality : 0.046 0.174 2808 Planarity : 0.004 0.052 3390 Dihedral : 5.161 54.367 2683 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.78 % Allowed : 17.16 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2444 helix: -1.34 (0.99), residues: 24 sheet: 0.83 (0.18), residues: 878 loop : -1.27 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 224 TYR 0.025 0.001 TYR L 49 PHE 0.016 0.002 PHE C 422 TRP 0.014 0.001 TRP B 178 HIS 0.004 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00434 (19258) covalent geometry : angle 0.55205 (26132) SS BOND : bond 0.00318 ( 40) SS BOND : angle 1.25122 ( 80) hydrogen bonds : bond 0.03352 ( 590) hydrogen bonds : angle 5.41886 ( 1632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 395 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8325 (ptt180) REVERT: B 292 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7356 (ttm-80) REVERT: D 318 CYS cc_start: 0.6865 (m) cc_final: 0.6526 (m) REVERT: K 91 TYR cc_start: 0.8611 (m-80) cc_final: 0.8153 (m-80) REVERT: R 36 TYR cc_start: 0.8747 (m-80) cc_final: 0.8492 (m-80) outliers start: 79 outliers final: 62 residues processed: 429 average time/residue: 0.5903 time to fit residues: 284.3673 Evaluate side-chains 452 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 388 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 167 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 226 GLN D 91 GLN H 100CASN I 100BGLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.124281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.116559 restraints weight = 23967.739| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.13 r_work: 0.3644 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19298 Z= 0.188 Angle : 0.560 7.627 26212 Z= 0.301 Chirality : 0.046 0.173 2808 Planarity : 0.004 0.045 3390 Dihedral : 5.142 52.543 2683 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.35 % Allowed : 17.83 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2444 helix: -1.31 (0.99), residues: 24 sheet: 0.83 (0.18), residues: 878 loop : -1.26 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 152 TYR 0.025 0.001 TYR L 49 PHE 0.016 0.002 PHE C 422 TRP 0.013 0.001 TRP B 178 HIS 0.004 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00436 (19258) covalent geometry : angle 0.55631 (26132) SS BOND : bond 0.00319 ( 40) SS BOND : angle 1.26817 ( 80) hydrogen bonds : bond 0.03349 ( 590) hydrogen bonds : angle 5.41511 ( 1632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 388 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8294 (ptt180) REVERT: B 292 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7354 (ttm-80) REVERT: D 318 CYS cc_start: 0.6854 (m) cc_final: 0.6529 (m) REVERT: K 91 TYR cc_start: 0.8606 (m-80) cc_final: 0.8148 (m-80) REVERT: R 36 TYR cc_start: 0.8735 (m-80) cc_final: 0.8486 (m-80) outliers start: 70 outliers final: 62 residues processed: 422 average time/residue: 0.5627 time to fit residues: 266.6856 Evaluate side-chains 446 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 382 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 176 optimal weight: 0.0270 chunk 21 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 42 optimal weight: 0.0980 chunk 141 optimal weight: 0.9990 chunk 107 optimal weight: 0.0770 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 226 GLN C 226 GLN D 91 GLN H 100CASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.126418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.118722 restraints weight = 23946.014| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.13 r_work: 0.3671 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19298 Z= 0.108 Angle : 0.509 7.087 26212 Z= 0.274 Chirality : 0.044 0.168 2808 Planarity : 0.004 0.046 3390 Dihedral : 4.862 57.258 2683 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.58 % Allowed : 18.74 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2444 helix: -1.06 (1.02), residues: 24 sheet: 0.86 (0.18), residues: 892 loop : -1.17 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 224 TYR 0.014 0.001 TYR L 49 PHE 0.015 0.001 PHE D 354 TRP 0.015 0.001 TRP A 178 HIS 0.003 0.001 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00242 (19258) covalent geometry : angle 0.50719 (26132) SS BOND : bond 0.00234 ( 40) SS BOND : angle 0.99146 ( 80) hydrogen bonds : bond 0.02917 ( 590) hydrogen bonds : angle 5.17935 ( 1632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 402 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7234 (ttm-80) REVERT: D 318 CYS cc_start: 0.6778 (m) cc_final: 0.6492 (m) REVERT: D 466 LEU cc_start: 0.8704 (mt) cc_final: 0.8487 (mp) REVERT: K 91 TYR cc_start: 0.8543 (m-80) cc_final: 0.8043 (m-80) REVERT: M 36 TYR cc_start: 0.8718 (m-80) cc_final: 0.8493 (m-80) outliers start: 54 outliers final: 43 residues processed: 429 average time/residue: 0.6041 time to fit residues: 290.7095 Evaluate side-chains 439 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 395 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 187 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 223 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN C 226 GLN D 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.125168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.117422 restraints weight = 23993.628| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.14 r_work: 0.3656 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19298 Z= 0.157 Angle : 0.539 7.089 26212 Z= 0.289 Chirality : 0.045 0.170 2808 Planarity : 0.004 0.045 3390 Dihedral : 4.950 55.606 2683 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.34 % Allowed : 19.55 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2444 helix: -0.86 (1.04), residues: 24 sheet: 0.87 (0.18), residues: 880 loop : -1.16 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.022 0.001 TYR L 49 PHE 0.015 0.002 PHE C 354 TRP 0.013 0.001 TRP B 178 HIS 0.004 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00362 (19258) covalent geometry : angle 0.53615 (26132) SS BOND : bond 0.00288 ( 40) SS BOND : angle 1.18423 ( 80) hydrogen bonds : bond 0.03167 ( 590) hydrogen bonds : angle 5.28536 ( 1632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7975.04 seconds wall clock time: 136 minutes 18.39 seconds (8178.39 seconds total)