Starting phenix.real_space_refine on Sun Aug 24 00:41:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t7a_41089/08_2025/8t7a_41089_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t7a_41089/08_2025/8t7a_41089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t7a_41089/08_2025/8t7a_41089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t7a_41089/08_2025/8t7a_41089.map" model { file = "/net/cci-nas-00/data/ceres_data/8t7a_41089/08_2025/8t7a_41089_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t7a_41089/08_2025/8t7a_41089_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.049 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 84 5.16 5 C 9990 2.51 5 N 2616 2.21 5 O 3129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15819 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "a" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2847 Classifications: {'peptide': 370} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "B" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "b" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2847 Classifications: {'peptide': 370} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "C" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "c" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2847 Classifications: {'peptide': 370} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "D" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "E" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Chain: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "G" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "I" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.76, per 1000 atoms: 0.24 Number of scatterers: 15819 At special positions: 0 Unit cell: (125.96, 124.08, 133.48, 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 84 16.00 O 3129 8.00 N 2616 7.00 C 9990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS a 439 " distance=2.04 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS a 212 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 343 " distance=2.02 Simple disulfide: pdb=" SG CYS a 322 " - pdb=" SG CYS a 333 " distance=2.03 Simple disulfide: pdb=" SG CYS a 358 " - pdb=" SG CYS a 367 " distance=2.03 Simple disulfide: pdb=" SG CYS a 382 " - pdb=" SG CYS a 393 " distance=2.03 Simple disulfide: pdb=" SG CYS a 416 " - pdb=" SG CYS a 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS b 439 " distance=2.02 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS b 212 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 343 " distance=2.05 Simple disulfide: pdb=" SG CYS b 322 " - pdb=" SG CYS b 333 " distance=2.03 Simple disulfide: pdb=" SG CYS b 358 " - pdb=" SG CYS b 367 " distance=2.03 Simple disulfide: pdb=" SG CYS b 382 " - pdb=" SG CYS b 393 " distance=2.03 Simple disulfide: pdb=" SG CYS b 416 " - pdb=" SG CYS b 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS c 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS c 212 " distance=2.03 Simple disulfide: pdb=" SG CYS c 313 " - pdb=" SG CYS c 343 " distance=2.05 Simple disulfide: pdb=" SG CYS c 322 " - pdb=" SG CYS c 333 " distance=2.02 Simple disulfide: pdb=" SG CYS c 358 " - pdb=" SG CYS c 367 " distance=2.03 Simple disulfide: pdb=" SG CYS c 382 " - pdb=" SG CYS c 393 " distance=2.03 Simple disulfide: pdb=" SG CYS c 416 " - pdb=" SG CYS c 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 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 Links applied NAG-ASN " NAG a 601 " - " ASN a 500 " " NAG b 601 " - " ASN b 500 " " NAG c 601 " - " ASN c 500 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 726.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 34 sheets defined 22.9% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 73 through 98 removed outlier: 3.518A pdb=" N LYS A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 138 through 142 Processing helix chain 'a' and resid 148 through 158 Processing helix chain 'a' and resid 162 through 171 Processing helix chain 'a' and resid 195 through 203 removed outlier: 3.726A pdb=" N LEU a 203 " --> pdb=" O ILE a 199 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 241 removed outlier: 4.485A pdb=" N VAL a 220 " --> pdb=" O ASN a 216 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG a 229 " --> pdb=" O GLN a 225 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU a 230 " --> pdb=" O LYS a 226 " (cutoff:3.500A) Processing helix chain 'a' and resid 253 through 264 Processing helix chain 'a' and resid 267 through 276 Processing helix chain 'a' and resid 277 through 284 Processing helix chain 'a' and resid 370 through 372 No H-bonds generated for 'chain 'a' and resid 370 through 372' Processing helix chain 'a' and resid 376 through 379 Processing helix chain 'a' and resid 380 through 385 removed outlier: 3.948A pdb=" N VAL a 384 " --> pdb=" O ASN a 380 " (cutoff:3.500A) Processing helix chain 'a' and resid 473 through 477 Processing helix chain 'a' and resid 492 through 503 Processing helix chain 'B' and resid 73 through 98 removed outlier: 3.518A pdb=" N LYS B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 138 through 142 Processing helix chain 'b' and resid 148 through 158 Processing helix chain 'b' and resid 162 through 171 Processing helix chain 'b' and resid 195 through 203 removed outlier: 3.726A pdb=" N LEU b 203 " --> pdb=" O ILE b 199 " (cutoff:3.500A) Processing helix chain 'b' and resid 216 through 241 removed outlier: 4.487A pdb=" N VAL b 220 " --> pdb=" O ASN b 216 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG b 229 " --> pdb=" O GLN b 225 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU b 230 " --> pdb=" O LYS b 226 " (cutoff:3.500A) Processing helix chain 'b' and resid 253 through 264 Processing helix chain 'b' and resid 267 through 276 Processing helix chain 'b' and resid 277 through 284 Processing helix chain 'b' and resid 370 through 372 No H-bonds generated for 'chain 'b' and resid 370 through 372' Processing helix chain 'b' and resid 376 through 379 Processing helix chain 'b' and resid 380 through 385 removed outlier: 3.948A pdb=" N VAL b 384 " --> pdb=" O ASN b 380 " (cutoff:3.500A) Processing helix chain 'b' and resid 473 through 478 Processing helix chain 'b' and resid 492 through 503 Processing helix chain 'C' and resid 73 through 98 removed outlier: 3.518A pdb=" N LYS C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 137 through 142 removed outlier: 4.482A pdb=" N PHE c 140 " --> pdb=" O PHE c 137 " (cutoff:3.500A) Processing helix chain 'c' and resid 148 through 158 Processing helix chain 'c' and resid 162 through 171 Processing helix chain 'c' and resid 195 through 203 removed outlier: 3.727A pdb=" N LEU c 203 " --> pdb=" O ILE c 199 " (cutoff:3.500A) Processing helix chain 'c' and resid 216 through 241 removed outlier: 4.485A pdb=" N VAL c 220 " --> pdb=" O ASN c 216 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG c 229 " --> pdb=" O GLN c 225 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU c 230 " --> pdb=" O LYS c 226 " (cutoff:3.500A) Processing helix chain 'c' and resid 253 through 264 Processing helix chain 'c' and resid 267 through 276 Processing helix chain 'c' and resid 277 through 284 Processing helix chain 'c' and resid 370 through 372 No H-bonds generated for 'chain 'c' and resid 370 through 372' Processing helix chain 'c' and resid 376 through 379 Processing helix chain 'c' and resid 380 through 385 removed outlier: 3.947A pdb=" N VAL c 384 " --> pdb=" O ASN c 380 " (cutoff:3.500A) Processing helix chain 'c' and resid 473 through 478 Processing helix chain 'c' and resid 492 through 503 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'a' and resid 359 through 361 removed outlier: 7.014A pdb=" N SER A 38 " --> pdb=" O THR a 318 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR a 318 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 40 " --> pdb=" O LEU a 316 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU a 316 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 42 " --> pdb=" O TRP a 314 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP a 314 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR A 44 " --> pdb=" O PRO a 312 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SER A 46 " --> pdb=" O ASP a 310 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL a 308 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 359 through 361 Processing sheet with id=AA3, first strand: chain 'a' and resid 176 through 180 removed outlier: 10.895A pdb=" N SER a 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR A 54 " --> pdb=" O SER a 186 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU a 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLU A 60 " --> pdb=" O VAL a 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP a 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL a 296 " --> pdb=" O ILE a 292 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE a 292 " --> pdb=" O VAL a 296 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA a 298 " --> pdb=" O SER a 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 321 through 322 removed outlier: 7.299A pdb=" N ILE a 395 " --> pdb=" O ASP a 489 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP a 489 " --> pdb=" O ILE a 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'a' and resid 430 through 435 removed outlier: 6.599A pdb=" N ALA a 424 " --> pdb=" O ILE a 432 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR a 434 " --> pdb=" O CYS a 422 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS a 422 " --> pdb=" O THR a 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 359 through 361 removed outlier: 7.071A pdb=" N SER B 38 " --> pdb=" O THR b 318 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR b 318 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 40 " --> pdb=" O LEU b 316 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU b 316 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS B 42 " --> pdb=" O TRP b 314 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP b 314 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 44 " --> pdb=" O PRO b 312 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER B 46 " --> pdb=" O ASP b 310 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL b 308 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 359 through 361 Processing sheet with id=AA9, first strand: chain 'b' and resid 176 through 180 removed outlier: 10.895A pdb=" N SER b 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR B 54 " --> pdb=" O SER b 186 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU b 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLU B 60 " --> pdb=" O VAL b 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP b 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL b 296 " --> pdb=" O ILE b 292 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE b 292 " --> pdb=" O VAL b 296 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA b 298 " --> pdb=" O SER b 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 321 through 322 removed outlier: 7.272A pdb=" N ILE b 395 " --> pdb=" O ASP b 489 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP b 489 " --> pdb=" O ILE b 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 404 through 407 Processing sheet with id=AB3, first strand: chain 'b' and resid 430 through 435 removed outlier: 6.599A pdb=" N ALA b 424 " --> pdb=" O ILE b 432 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR b 434 " --> pdb=" O CYS b 422 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS b 422 " --> pdb=" O THR b 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 359 through 361 removed outlier: 6.991A pdb=" N SER C 38 " --> pdb=" O THR c 318 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR c 318 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 40 " --> pdb=" O LEU c 316 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU c 316 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS C 42 " --> pdb=" O TRP c 314 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP c 314 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR C 44 " --> pdb=" O PRO c 312 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SER C 46 " --> pdb=" O ASP c 310 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL c 308 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 359 through 361 Processing sheet with id=AB6, first strand: chain 'c' and resid 176 through 180 removed outlier: 10.895A pdb=" N SER c 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR C 54 " --> pdb=" O SER c 186 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU c 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU C 60 " --> pdb=" O VAL c 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP c 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL c 296 " --> pdb=" O ILE c 292 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE c 292 " --> pdb=" O VAL c 296 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA c 298 " --> pdb=" O SER c 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 321 through 322 removed outlier: 7.289A pdb=" N ILE c 395 " --> pdb=" O ASP c 489 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP c 489 " --> pdb=" O ILE c 395 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'c' and resid 430 through 435 removed outlier: 6.600A pdb=" N ALA c 424 " --> pdb=" O ILE c 432 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR c 434 " --> pdb=" O CYS c 422 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS c 422 " --> pdb=" O THR c 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.521A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY D 33 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR D 32 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER D 52 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.607A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.523A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 27C through 27D Processing sheet with id=AC7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.522A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR F 32 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER F 52 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.606A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.523A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 27C through 27D Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.521A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR H 32 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.607A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.523A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 27C through 27D 766 hydrogen bonds defined for protein. 1953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2630 1.30 - 1.43: 4003 1.43 - 1.56: 9345 1.56 - 1.69: 3 1.69 - 1.82: 114 Bond restraints: 16095 Sorted by residual: bond pdb=" C VAL a 406 " pdb=" O VAL a 406 " ideal model delta sigma weight residual 1.237 1.166 0.072 1.08e-02 8.57e+03 4.42e+01 bond pdb=" C ILE c 332 " pdb=" O ILE c 332 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.02e-02 9.61e+03 3.91e+01 bond pdb=" C SER a 415 " pdb=" O SER a 415 " ideal model delta sigma weight residual 1.235 1.168 0.068 1.19e-02 7.06e+03 3.23e+01 bond pdb=" N TYR c 417 " pdb=" CA TYR c 417 " ideal model delta sigma weight residual 1.455 1.384 0.070 1.26e-02 6.30e+03 3.10e+01 bond pdb=" C THR a 335 " pdb=" O THR a 335 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.26e-02 6.30e+03 3.04e+01 ... (remaining 16090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 21437 2.34 - 4.68: 349 4.68 - 7.02: 53 7.02 - 9.36: 11 9.36 - 11.70: 2 Bond angle restraints: 21852 Sorted by residual: angle pdb=" N CYS c 333 " pdb=" CA CYS c 333 " pdb=" C CYS c 333 " ideal model delta sigma weight residual 109.81 121.51 -11.70 1.53e+00 4.27e-01 5.85e+01 angle pdb=" N CYS b 333 " pdb=" CA CYS b 333 " pdb=" C CYS b 333 " ideal model delta sigma weight residual 109.52 120.27 -10.75 1.55e+00 4.16e-01 4.81e+01 angle pdb=" N SER c 275 " pdb=" CA SER c 275 " pdb=" C SER c 275 " ideal model delta sigma weight residual 111.71 104.48 7.23 1.15e+00 7.56e-01 3.95e+01 angle pdb=" N SER a 275 " pdb=" CA SER a 275 " pdb=" C SER a 275 " ideal model delta sigma weight residual 111.71 104.51 7.20 1.15e+00 7.56e-01 3.92e+01 angle pdb=" N SER b 275 " pdb=" CA SER b 275 " pdb=" C SER b 275 " ideal model delta sigma weight residual 111.71 104.52 7.19 1.15e+00 7.56e-01 3.91e+01 ... (remaining 21847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 8942 17.11 - 34.21: 608 34.21 - 51.32: 183 51.32 - 68.43: 49 68.43 - 85.54: 13 Dihedral angle restraints: 9795 sinusoidal: 3858 harmonic: 5937 Sorted by residual: dihedral pdb=" CB CYS b 358 " pdb=" SG CYS b 358 " pdb=" SG CYS b 367 " pdb=" CB CYS b 367 " ideal model delta sinusoidal sigma weight residual 93.00 128.74 -35.74 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CB CYS c 358 " pdb=" SG CYS c 358 " pdb=" SG CYS c 367 " pdb=" CB CYS c 367 " ideal model delta sinusoidal sigma weight residual 93.00 128.74 -35.74 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CB CYS a 358 " pdb=" SG CYS a 358 " pdb=" SG CYS a 367 " pdb=" CB CYS a 367 " ideal model delta sinusoidal sigma weight residual 93.00 128.70 -35.70 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 9792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2485 0.109 - 0.217: 83 0.217 - 0.326: 3 0.326 - 0.434: 0 0.434 - 0.543: 3 Chirality restraints: 2574 Sorted by residual: chirality pdb=" CG LEU c 158 " pdb=" CB LEU c 158 " pdb=" CD1 LEU c 158 " pdb=" CD2 LEU c 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" CG LEU b 158 " pdb=" CB LEU b 158 " pdb=" CD1 LEU b 158 " pdb=" CD2 LEU b 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CG LEU a 158 " pdb=" CB LEU a 158 " pdb=" CD1 LEU a 158 " pdb=" CD2 LEU a 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 2571 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 81 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" CD GLN A 81 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLN A 81 " -0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN A 81 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 81 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" CD GLN C 81 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLN C 81 " -0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN C 81 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 81 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" CD GLN B 81 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLN B 81 " -0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN B 81 " -0.019 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1480 2.75 - 3.29: 15149 3.29 - 3.82: 26191 3.82 - 4.36: 32319 4.36 - 4.90: 56521 Nonbonded interactions: 131660 Sorted by model distance: nonbonded pdb=" OG SER b 290 " pdb=" O ALA b 298 " model vdw 2.212 3.040 nonbonded pdb=" OG SER a 290 " pdb=" O ALA a 298 " model vdw 2.213 3.040 nonbonded pdb=" OG SER c 290 " pdb=" O ALA c 298 " model vdw 2.213 3.040 nonbonded pdb=" O SER D 7 " pdb=" OG1 THR D 107 " model vdw 2.263 3.040 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 107 " model vdw 2.263 3.040 ... (remaining 131655 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.005 0.072 16125 Z= 0.363 Angle : 0.716 11.698 21915 Z= 0.417 Chirality : 0.050 0.543 2574 Planarity : 0.006 0.081 2757 Dihedral : 13.491 85.537 5904 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.66 % Allowed : 11.44 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.19), residues: 2016 helix: 0.86 (0.27), residues: 366 sheet: 0.52 (0.20), residues: 684 loop : 0.06 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 66 TYR 0.018 0.002 TYR c 417 PHE 0.030 0.002 PHE b 140 TRP 0.018 0.001 TRP B 52 HIS 0.005 0.002 HIS b 159 Details of bonding type rmsd covalent geometry : bond 0.00537 (16095) covalent geometry : angle 0.71415 (21852) SS BOND : bond 0.00594 ( 27) SS BOND : angle 1.35028 ( 54) hydrogen bonds : bond 0.13951 ( 732) hydrogen bonds : angle 7.26651 ( 1953) link_NAG-ASN : bond 0.00151 ( 3) link_NAG-ASN : angle 0.81585 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8044 (ttpp) cc_final: 0.7601 (mttp) REVERT: A 88 ASN cc_start: 0.8268 (m-40) cc_final: 0.7977 (m-40) REVERT: B 87 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7537 (mttp) REVERT: b 264 MET cc_start: 0.8731 (mtp) cc_final: 0.8483 (mtm) REVERT: b 429 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7709 (mtp180) REVERT: b 465 LYS cc_start: 0.8173 (tmtt) cc_final: 0.7518 (tttm) REVERT: C 87 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7534 (mttp) REVERT: C 88 ASN cc_start: 0.8168 (m-40) cc_final: 0.7954 (m-40) REVERT: c 202 GLN cc_start: 0.7934 (mt0) cc_final: 0.7625 (mt0) REVERT: c 465 LYS cc_start: 0.8264 (tmtt) cc_final: 0.7566 (tttm) REVERT: H 3 GLN cc_start: 0.8536 (pt0) cc_final: 0.8302 (pt0) REVERT: I 89 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8295 (tt0) outliers start: 12 outliers final: 6 residues processed: 226 average time/residue: 0.5173 time to fit residues: 129.4297 Evaluate side-chains 171 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 404 SER Chi-restraints excluded: chain b residue 161 GLU Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 89 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 277 ASN b 317 HIS D 58 ASN G 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129573 restraints weight = 16521.050| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.02 r_work: 0.3254 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16125 Z= 0.173 Angle : 0.537 8.397 21915 Z= 0.286 Chirality : 0.044 0.149 2574 Planarity : 0.004 0.054 2757 Dihedral : 5.481 52.940 2260 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.04 % Allowed : 12.55 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.19), residues: 2016 helix: 2.08 (0.27), residues: 372 sheet: 0.69 (0.20), residues: 675 loop : 0.05 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG b 282 TYR 0.023 0.002 TYR H 100E PHE 0.009 0.001 PHE b 137 TRP 0.012 0.002 TRP F 36 HIS 0.005 0.001 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00410 (16095) covalent geometry : angle 0.53582 (21852) SS BOND : bond 0.00567 ( 27) SS BOND : angle 0.97784 ( 54) hydrogen bonds : bond 0.04085 ( 732) hydrogen bonds : angle 5.33607 ( 1953) link_NAG-ASN : bond 0.00201 ( 3) link_NAG-ASN : angle 0.62191 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7753 (ttmt) REVERT: a 272 LYS cc_start: 0.7628 (tttm) cc_final: 0.7426 (ttpp) REVERT: a 324 THR cc_start: 0.8539 (p) cc_final: 0.8175 (p) REVERT: B 87 LYS cc_start: 0.8121 (ttpp) cc_final: 0.7685 (ttmt) REVERT: b 429 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7661 (mtp180) REVERT: b 465 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7547 (tttm) REVERT: C 31 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: C 77 LYS cc_start: 0.8090 (mttm) cc_final: 0.7694 (mmtt) REVERT: C 87 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7862 (ttpt) REVERT: c 202 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7428 (mt0) REVERT: c 324 THR cc_start: 0.8263 (p) cc_final: 0.8058 (p) REVERT: c 465 LYS cc_start: 0.8424 (tmtt) cc_final: 0.7606 (tttm) REVERT: c 498 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7755 (mtpt) outliers start: 55 outliers final: 24 residues processed: 221 average time/residue: 0.5325 time to fit residues: 130.0874 Evaluate side-chains 200 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 384 VAL Chi-restraints excluded: chain a residue 396 MET Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 384 VAL Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 170 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 172 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 146 optimal weight: 0.0470 chunk 189 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 34 GLN C 98 GLN D 58 ASN I 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.165639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131922 restraints weight = 16644.516| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.02 r_work: 0.3292 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16125 Z= 0.112 Angle : 0.470 7.852 21915 Z= 0.248 Chirality : 0.042 0.147 2574 Planarity : 0.003 0.040 2757 Dihedral : 4.976 53.586 2250 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.49 % Allowed : 13.88 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.19), residues: 2016 helix: 2.48 (0.27), residues: 372 sheet: 0.80 (0.20), residues: 675 loop : 0.05 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 61 TYR 0.014 0.001 TYR c 299 PHE 0.008 0.001 PHE b 137 TRP 0.010 0.001 TRP F 36 HIS 0.004 0.001 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00258 (16095) covalent geometry : angle 0.46968 (21852) SS BOND : bond 0.00254 ( 27) SS BOND : angle 0.68008 ( 54) hydrogen bonds : bond 0.03362 ( 732) hydrogen bonds : angle 5.02741 ( 1953) link_NAG-ASN : bond 0.00175 ( 3) link_NAG-ASN : angle 0.79121 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7759 (ttmt) REVERT: a 202 GLN cc_start: 0.7910 (mt0) cc_final: 0.7627 (mt0) REVERT: a 324 THR cc_start: 0.8458 (p) cc_final: 0.8089 (p) REVERT: B 87 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7650 (ttmt) REVERT: b 263 ASP cc_start: 0.8172 (m-30) cc_final: 0.7920 (m-30) REVERT: b 289 MET cc_start: 0.8454 (tpt) cc_final: 0.7788 (tpt) REVERT: b 429 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7690 (mtp180) REVERT: b 465 LYS cc_start: 0.8270 (tmtt) cc_final: 0.7494 (tttm) REVERT: C 77 LYS cc_start: 0.7986 (mttm) cc_final: 0.7594 (mmtt) REVERT: C 87 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7916 (ttpt) REVERT: c 465 LYS cc_start: 0.8394 (tmtt) cc_final: 0.7568 (tttm) REVERT: D 46 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: F 46 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: F 69 MET cc_start: 0.8761 (mtt) cc_final: 0.8450 (mtm) REVERT: G 89 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: I 61 ARG cc_start: 0.7162 (ptt-90) cc_final: 0.6936 (ptt-90) outliers start: 45 outliers final: 30 residues processed: 218 average time/residue: 0.5195 time to fit residues: 124.9449 Evaluate side-chains 208 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 136 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN b 277 ASN C 34 GLN C 98 GLN D 58 ASN I 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.159839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125345 restraints weight = 16605.347| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.08 r_work: 0.3179 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16125 Z= 0.274 Angle : 0.612 9.359 21915 Z= 0.321 Chirality : 0.048 0.149 2574 Planarity : 0.004 0.043 2757 Dihedral : 5.509 54.198 2250 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.53 % Allowed : 13.32 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.19), residues: 2016 helix: 2.10 (0.27), residues: 372 sheet: 0.73 (0.21), residues: 621 loop : -0.34 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 49 TYR 0.023 0.002 TYR c 457 PHE 0.014 0.002 PHE b 137 TRP 0.015 0.003 TRP F 36 HIS 0.007 0.002 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00668 (16095) covalent geometry : angle 0.61080 (21852) SS BOND : bond 0.00545 ( 27) SS BOND : angle 1.04284 ( 54) hydrogen bonds : bond 0.04648 ( 732) hydrogen bonds : angle 5.47360 ( 1953) link_NAG-ASN : bond 0.00171 ( 3) link_NAG-ASN : angle 0.81974 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 179 time to evaluate : 0.444 Fit side-chains REVERT: A 87 LYS cc_start: 0.8408 (ttpp) cc_final: 0.7863 (ttmt) REVERT: B 87 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7712 (ttmt) REVERT: b 180 SER cc_start: 0.8878 (p) cc_final: 0.8575 (p) REVERT: b 202 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7291 (mt0) REVERT: b 429 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7786 (mtp180) REVERT: b 465 LYS cc_start: 0.8411 (tmtt) cc_final: 0.7672 (tttm) REVERT: b 498 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7573 (mtpt) REVERT: C 87 LYS cc_start: 0.8292 (ttpp) cc_final: 0.8004 (ttpt) REVERT: c 202 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: c 297 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8064 (tp) REVERT: c 465 LYS cc_start: 0.8461 (tmtt) cc_final: 0.7681 (tttm) REVERT: c 498 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7649 (mtpt) REVERT: D 46 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6877 (tm-30) REVERT: D 96 ARG cc_start: 0.7954 (ptt-90) cc_final: 0.7690 (ptm-80) REVERT: F 46 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: F 69 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8555 (mtm) REVERT: F 81 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6478 (tm-30) REVERT: G 61 ARG cc_start: 0.7322 (ptt-90) cc_final: 0.7055 (ptt-90) REVERT: G 89 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8399 (pt0) REVERT: I 61 ARG cc_start: 0.7343 (ptt-90) cc_final: 0.7043 (ptt-90) outliers start: 82 outliers final: 50 residues processed: 233 average time/residue: 0.5220 time to fit residues: 134.3803 Evaluate side-chains 236 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain b residue 176 LYS Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 202 GLN Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain c residue 164 VAL Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 384 VAL Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 105 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN b 277 ASN C 34 GLN C 98 GLN G 55 GLN I 42 GLN I 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129183 restraints weight = 16529.131| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.03 r_work: 0.3248 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16125 Z= 0.148 Angle : 0.503 8.708 21915 Z= 0.265 Chirality : 0.043 0.151 2574 Planarity : 0.004 0.049 2757 Dihedral : 5.198 53.837 2250 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.87 % Allowed : 14.59 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.19), residues: 2016 helix: 2.33 (0.27), residues: 372 sheet: 0.60 (0.20), residues: 672 loop : -0.23 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.015 0.002 TYR c 457 PHE 0.010 0.001 PHE b 137 TRP 0.011 0.002 TRP H 36 HIS 0.005 0.001 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00351 (16095) covalent geometry : angle 0.50208 (21852) SS BOND : bond 0.00271 ( 27) SS BOND : angle 0.83068 ( 54) hydrogen bonds : bond 0.03636 ( 732) hydrogen bonds : angle 5.16039 ( 1953) link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 0.81882 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 0.669 Fit side-chains REVERT: A 87 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7707 (ttmt) REVERT: B 87 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7652 (ttmt) REVERT: b 165 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7706 (m110) REVERT: b 180 SER cc_start: 0.8862 (p) cc_final: 0.8554 (p) REVERT: b 289 MET cc_start: 0.8547 (tpt) cc_final: 0.7826 (tpt) REVERT: b 429 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7533 (mtm110) REVERT: b 465 LYS cc_start: 0.8293 (tmtt) cc_final: 0.7532 (tttm) REVERT: b 498 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7454 (mtpt) REVERT: C 77 LYS cc_start: 0.8106 (mttm) cc_final: 0.7650 (mmtt) REVERT: C 87 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7858 (ttpt) REVERT: c 202 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: c 465 LYS cc_start: 0.8375 (tmtt) cc_final: 0.7573 (tttm) REVERT: c 498 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7537 (mtpt) REVERT: D 46 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: D 96 ARG cc_start: 0.7758 (ptt-90) cc_final: 0.7425 (ptm-80) REVERT: E 89 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: F 46 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: F 69 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8478 (mtm) REVERT: G 61 ARG cc_start: 0.7157 (ptt-90) cc_final: 0.6821 (ptt-90) REVERT: G 89 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: H 46 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6527 (tm-30) REVERT: I 61 ARG cc_start: 0.7240 (ptt-90) cc_final: 0.6952 (ptt-90) outliers start: 70 outliers final: 46 residues processed: 230 average time/residue: 0.5132 time to fit residues: 130.6208 Evaluate side-chains 228 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain b residue 501 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 12 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 73 optimal weight: 0.8980 chunk 159 optimal weight: 0.3980 chunk 195 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN C 34 GLN C 98 GLN E 55 GLN I 42 GLN I 55 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127927 restraints weight = 16496.205| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.03 r_work: 0.3226 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16125 Z= 0.181 Angle : 0.529 9.334 21915 Z= 0.278 Chirality : 0.044 0.147 2574 Planarity : 0.004 0.051 2757 Dihedral : 5.293 54.368 2250 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.31 % Allowed : 14.48 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.19), residues: 2016 helix: 2.32 (0.27), residues: 372 sheet: 0.51 (0.20), residues: 672 loop : -0.29 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.018 0.002 TYR c 457 PHE 0.011 0.001 PHE b 137 TRP 0.012 0.002 TRP F 36 HIS 0.005 0.001 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00435 (16095) covalent geometry : angle 0.52758 (21852) SS BOND : bond 0.00340 ( 27) SS BOND : angle 0.86805 ( 54) hydrogen bonds : bond 0.03896 ( 732) hydrogen bonds : angle 5.22358 ( 1953) link_NAG-ASN : bond 0.00158 ( 3) link_NAG-ASN : angle 0.83578 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 176 time to evaluate : 0.653 Fit side-chains REVERT: A 87 LYS cc_start: 0.8353 (ttpp) cc_final: 0.7798 (ttmt) REVERT: a 202 GLN cc_start: 0.7965 (mt0) cc_final: 0.7715 (mt0) REVERT: B 87 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7739 (ttmt) REVERT: b 165 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7802 (m110) REVERT: b 180 SER cc_start: 0.8871 (p) cc_final: 0.8570 (p) REVERT: b 272 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7329 (tttm) REVERT: b 429 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7614 (mtm110) REVERT: b 465 LYS cc_start: 0.8349 (tmtt) cc_final: 0.7620 (tttm) REVERT: b 498 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7494 (mtpt) REVERT: C 77 LYS cc_start: 0.8187 (mttm) cc_final: 0.7741 (mmtt) REVERT: C 87 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7894 (ttpt) REVERT: c 202 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7533 (mt0) REVERT: c 297 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8022 (tp) REVERT: c 465 LYS cc_start: 0.8423 (tmtt) cc_final: 0.7652 (tttm) REVERT: c 498 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7635 (mtpt) REVERT: D 46 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: D 96 ARG cc_start: 0.7882 (ptt-90) cc_final: 0.7568 (ptm-80) REVERT: E 89 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: F 46 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: F 69 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8517 (mtm) REVERT: F 81 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6332 (tm-30) REVERT: G 89 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: H 46 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6590 (tm-30) REVERT: I 61 ARG cc_start: 0.7297 (ptt-90) cc_final: 0.6951 (ptt-90) outliers start: 78 outliers final: 53 residues processed: 230 average time/residue: 0.5296 time to fit residues: 134.6035 Evaluate side-chains 239 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain a residue 501 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 222 GLU Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 272 LYS Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 164 VAL Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 19 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN C 34 GLN C 98 GLN E 55 GLN I 42 GLN I 55 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129898 restraints weight = 16353.850| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.99 r_work: 0.3261 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16125 Z= 0.131 Angle : 0.486 10.078 21915 Z= 0.256 Chirality : 0.043 0.150 2574 Planarity : 0.004 0.051 2757 Dihedral : 5.102 53.937 2250 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.09 % Allowed : 14.98 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.19), residues: 2016 helix: 2.50 (0.27), residues: 372 sheet: 0.58 (0.20), residues: 672 loop : -0.28 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 49 TYR 0.015 0.001 TYR a 457 PHE 0.009 0.001 PHE b 137 TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00309 (16095) covalent geometry : angle 0.48547 (21852) SS BOND : bond 0.00242 ( 27) SS BOND : angle 0.73804 ( 54) hydrogen bonds : bond 0.03416 ( 732) hydrogen bonds : angle 5.04294 ( 1953) link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 0.82661 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 180 time to evaluate : 0.579 Fit side-chains REVERT: A 87 LYS cc_start: 0.8311 (ttpp) cc_final: 0.7750 (ttmt) REVERT: a 202 GLN cc_start: 0.7970 (mt0) cc_final: 0.7654 (mt0) REVERT: B 87 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7682 (ttmt) REVERT: b 180 SER cc_start: 0.8850 (p) cc_final: 0.8551 (p) REVERT: b 429 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7572 (mtm110) REVERT: b 465 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7552 (tttm) REVERT: b 498 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7521 (mtpt) REVERT: C 87 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7935 (ttpt) REVERT: c 202 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: c 465 LYS cc_start: 0.8393 (tmtt) cc_final: 0.7608 (tttm) REVERT: c 498 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7561 (mtpt) REVERT: D 46 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: D 96 ARG cc_start: 0.7745 (ptt-90) cc_final: 0.7426 (ptm-80) REVERT: E 89 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: F 46 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6555 (tm-30) REVERT: F 69 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8487 (mtm) REVERT: G 61 ARG cc_start: 0.7086 (ptt-90) cc_final: 0.6874 (ptt-90) REVERT: G 89 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: H 46 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: I 61 ARG cc_start: 0.7205 (ptt-90) cc_final: 0.6856 (ptt-90) outliers start: 74 outliers final: 57 residues processed: 232 average time/residue: 0.5762 time to fit residues: 147.3769 Evaluate side-chains 236 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain a residue 501 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain b residue 501 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 212 CYS Chi-restraints excluded: chain c residue 239 VAL Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 34 GLN C 98 GLN D 58 ASN I 42 GLN I 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.161341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127645 restraints weight = 16572.443| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.06 r_work: 0.3222 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16125 Z= 0.199 Angle : 0.547 10.817 21915 Z= 0.287 Chirality : 0.045 0.147 2574 Planarity : 0.004 0.052 2757 Dihedral : 5.336 54.568 2250 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.37 % Allowed : 15.20 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.19), residues: 2016 helix: 2.34 (0.27), residues: 372 sheet: 0.48 (0.20), residues: 672 loop : -0.35 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.019 0.002 TYR c 457 PHE 0.011 0.001 PHE a 483 TRP 0.013 0.002 TRP F 36 HIS 0.006 0.001 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00480 (16095) covalent geometry : angle 0.54582 (21852) SS BOND : bond 0.00373 ( 27) SS BOND : angle 0.87955 ( 54) hydrogen bonds : bond 0.04013 ( 732) hydrogen bonds : angle 5.25648 ( 1953) link_NAG-ASN : bond 0.00172 ( 3) link_NAG-ASN : angle 0.85946 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 0.584 Fit side-chains REVERT: A 87 LYS cc_start: 0.8339 (ttpp) cc_final: 0.7775 (ttmt) REVERT: a 202 GLN cc_start: 0.7987 (mt0) cc_final: 0.7719 (mt0) REVERT: B 87 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7688 (ttmt) REVERT: b 180 SER cc_start: 0.8855 (p) cc_final: 0.8550 (p) REVERT: b 272 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7303 (tttm) REVERT: b 429 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7659 (mtp180) REVERT: b 465 LYS cc_start: 0.8335 (tmtt) cc_final: 0.7601 (tttm) REVERT: b 498 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7529 (mtpt) REVERT: c 202 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: c 297 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8064 (tp) REVERT: c 465 LYS cc_start: 0.8406 (tmtt) cc_final: 0.7631 (tttm) REVERT: c 498 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7612 (mtpt) REVERT: D 46 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6826 (tm-30) REVERT: D 96 ARG cc_start: 0.7875 (ptt-90) cc_final: 0.7577 (ptm-80) REVERT: E 89 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: F 46 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: F 69 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8524 (mtm) REVERT: F 81 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6332 (tm-30) REVERT: G 61 ARG cc_start: 0.7161 (ptt-90) cc_final: 0.6814 (ptt-90) REVERT: G 89 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: H 46 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6586 (tm-30) REVERT: I 61 ARG cc_start: 0.7214 (ptt-90) cc_final: 0.6821 (ptt-90) outliers start: 79 outliers final: 56 residues processed: 224 average time/residue: 0.5429 time to fit residues: 134.1229 Evaluate side-chains 239 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain a residue 501 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 272 LYS Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 239 VAL Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.0370 chunk 98 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 3 optimal weight: 0.0770 chunk 192 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN C 34 GLN C 98 GLN I 42 GLN I 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.166320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133144 restraints weight = 16441.919| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.01 r_work: 0.3313 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16125 Z= 0.090 Angle : 0.455 11.261 21915 Z= 0.239 Chirality : 0.042 0.144 2574 Planarity : 0.003 0.053 2757 Dihedral : 4.890 53.599 2250 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.99 % Allowed : 17.03 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.19), residues: 2016 helix: 2.71 (0.27), residues: 372 sheet: 0.67 (0.20), residues: 675 loop : -0.22 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG a 429 TYR 0.012 0.001 TYR b 299 PHE 0.006 0.001 PHE b 137 TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00200 (16095) covalent geometry : angle 0.45464 (21852) SS BOND : bond 0.00173 ( 27) SS BOND : angle 0.61544 ( 54) hydrogen bonds : bond 0.02899 ( 732) hydrogen bonds : angle 4.80936 ( 1953) link_NAG-ASN : bond 0.00149 ( 3) link_NAG-ASN : angle 0.86432 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.436 Fit side-chains REVERT: A 77 LYS cc_start: 0.8027 (mttm) cc_final: 0.7435 (mmtt) REVERT: A 87 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7612 (ttmt) REVERT: a 185 VAL cc_start: 0.7861 (t) cc_final: 0.7502 (p) REVERT: a 202 GLN cc_start: 0.7892 (mt0) cc_final: 0.7489 (mt0) REVERT: B 87 LYS cc_start: 0.8114 (ttpp) cc_final: 0.7833 (ttpp) REVERT: b 272 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7135 (tttm) REVERT: b 294 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7443 (mt-10) REVERT: b 429 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7611 (mtp180) REVERT: b 465 LYS cc_start: 0.8245 (tmtt) cc_final: 0.7831 (tptm) REVERT: b 498 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7381 (mtpt) REVERT: C 87 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7618 (mttt) REVERT: c 465 LYS cc_start: 0.8383 (tmtt) cc_final: 0.7582 (tttm) REVERT: D 58 ASN cc_start: 0.8546 (t0) cc_final: 0.8232 (t0) REVERT: E 89 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: F 69 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8446 (mtm) REVERT: F 81 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: F 105 GLN cc_start: 0.8632 (pm20) cc_final: 0.8385 (pm20) REVERT: G 61 ARG cc_start: 0.6993 (ptt-90) cc_final: 0.6727 (ptt-90) REVERT: G 89 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: H 46 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: H 105 GLN cc_start: 0.8648 (pm20) cc_final: 0.8417 (pm20) outliers start: 54 outliers final: 41 residues processed: 224 average time/residue: 0.5444 time to fit residues: 134.9672 Evaluate side-chains 215 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 272 LYS Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 212 CYS Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 chunk 70 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 150 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 157 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 380 ASN b 225 GLN C 98 GLN I 42 GLN I 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132417 restraints weight = 16456.201| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.01 r_work: 0.3294 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16125 Z= 0.102 Angle : 0.470 11.951 21915 Z= 0.245 Chirality : 0.042 0.143 2574 Planarity : 0.003 0.053 2757 Dihedral : 4.903 53.840 2250 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.60 % Allowed : 17.41 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 2016 helix: 2.77 (0.27), residues: 372 sheet: 0.69 (0.20), residues: 675 loop : -0.19 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG a 429 TYR 0.013 0.001 TYR a 457 PHE 0.007 0.001 PHE b 137 TRP 0.016 0.001 TRP H 50 HIS 0.003 0.001 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00235 (16095) covalent geometry : angle 0.46887 (21852) SS BOND : bond 0.00218 ( 27) SS BOND : angle 0.80838 ( 54) hydrogen bonds : bond 0.03042 ( 732) hydrogen bonds : angle 4.78701 ( 1953) link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 0.77885 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.446 Fit side-chains REVERT: A 87 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7625 (ttmt) REVERT: a 185 VAL cc_start: 0.7842 (t) cc_final: 0.7478 (p) REVERT: a 202 GLN cc_start: 0.7929 (mt0) cc_final: 0.7537 (mt0) REVERT: B 77 LYS cc_start: 0.8057 (mttm) cc_final: 0.7468 (mmtt) REVERT: b 294 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7451 (mt-10) REVERT: b 429 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7621 (mtp180) REVERT: b 465 LYS cc_start: 0.8279 (tmtt) cc_final: 0.7504 (tttm) REVERT: b 498 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7415 (mtpt) REVERT: C 87 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7652 (mttt) REVERT: c 465 LYS cc_start: 0.8373 (tmtt) cc_final: 0.7576 (tttm) REVERT: F 69 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8461 (mtm) REVERT: F 81 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: F 105 GLN cc_start: 0.8655 (pm20) cc_final: 0.8415 (pm20) REVERT: G 61 ARG cc_start: 0.6999 (ptt-90) cc_final: 0.6704 (ptt-90) REVERT: G 89 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: H 46 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6532 (tm-30) outliers start: 47 outliers final: 39 residues processed: 201 average time/residue: 0.5728 time to fit residues: 126.6750 Evaluate side-chains 209 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 55 optimal weight: 0.0670 chunk 177 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 133 optimal weight: 8.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 98 GLN D 58 ASN I 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.164727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129720 restraints weight = 15685.021| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.88 r_work: 0.3236 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16125 Z= 0.086 Angle : 0.454 11.989 21915 Z= 0.236 Chirality : 0.041 0.141 2574 Planarity : 0.003 0.053 2757 Dihedral : 4.688 53.517 2247 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.49 % Allowed : 17.74 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.19), residues: 2016 helix: 2.88 (0.27), residues: 372 sheet: 0.68 (0.21), residues: 654 loop : -0.15 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 61 TYR 0.013 0.001 TYR b 299 PHE 0.005 0.001 PHE b 137 TRP 0.017 0.001 TRP H 50 HIS 0.002 0.001 HIS a 317 Details of bonding type rmsd covalent geometry : bond 0.00193 (16095) covalent geometry : angle 0.45262 (21852) SS BOND : bond 0.00193 ( 27) SS BOND : angle 0.73317 ( 54) hydrogen bonds : bond 0.02764 ( 732) hydrogen bonds : angle 4.64745 ( 1953) link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 0.75501 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5202.10 seconds wall clock time: 89 minutes 23.01 seconds (5363.01 seconds total)