Starting phenix.real_space_refine on Sat Jun 14 04:57:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t7a_41089/06_2025/8t7a_41089_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t7a_41089/06_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_41089/06_2025/8t7a_41089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t7a_41089/06_2025/8t7a_41089.map" model { file = "/net/cci-nas-00/data/ceres_data/8t7a_41089/06_2025/8t7a_41089_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t7a_41089/06_2025/8t7a_41089_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.26, per 1000 atoms: 0.65 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: 3.73 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.43 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: 7.03 Time building geometry restraints manager: 4.43 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: 0.08 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: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.420 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:18.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.018 0.001 TRP B 52 HIS 0.005 0.002 HIS b 159 PHE 0.030 0.002 PHE b 140 TYR 0.018 0.002 TYR c 417 ARG 0.015 0.001 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 3) link_NAG-ASN : angle 0.81585 ( 9) hydrogen bonds : bond 0.13951 ( 732) hydrogen bonds : angle 7.26651 ( 1953) SS BOND : bond 0.00594 ( 27) SS BOND : angle 1.35028 ( 54) covalent geometry : bond 0.00537 (16095) covalent geometry : angle 0.71415 (21852) *********************** 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 : 1.803 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 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: 1.2493 time to fit residues: 312.6570 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 : 1.683 ------------------------------------------------------------------------------- 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 169 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 102 optimal weight: 0.0040 chunk 81 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 117 optimal weight: 0.0270 chunk 182 optimal weight: 6.9990 overall best weight: 0.9252 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.164697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131065 restraints weight = 16386.729| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.02 r_work: 0.3278 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16125 Z= 0.146 Angle : 0.515 8.506 21915 Z= 0.273 Chirality : 0.043 0.148 2574 Planarity : 0.004 0.051 2757 Dihedral : 5.394 52.878 2260 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.10 % Allowed : 12.33 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2016 helix: 2.18 (0.27), residues: 372 sheet: 0.73 (0.20), residues: 681 loop : 0.07 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 36 HIS 0.004 0.001 HIS a 317 PHE 0.008 0.001 PHE b 137 TYR 0.021 0.002 TYR H 100E ARG 0.002 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 0.67717 ( 9) hydrogen bonds : bond 0.03826 ( 732) hydrogen bonds : angle 5.24413 ( 1953) SS BOND : bond 0.00348 ( 27) SS BOND : angle 0.91555 ( 54) covalent geometry : bond 0.00343 (16095) covalent geometry : angle 0.51361 (21852) *********************** 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 244 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 2.712 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7714 (ttmt) REVERT: a 202 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: a 324 THR cc_start: 0.8509 (p) cc_final: 0.8134 (p) REVERT: B 87 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7590 (ttmt) REVERT: b 289 MET cc_start: 0.8479 (tpt) cc_final: 0.8243 (tpt) REVERT: b 429 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7630 (mtp180) REVERT: b 465 LYS cc_start: 0.8258 (tmtt) cc_final: 0.7497 (tttm) REVERT: C 31 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: C 77 LYS cc_start: 0.8008 (mttm) cc_final: 0.7621 (mmtt) REVERT: C 87 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7890 (ttpt) REVERT: c 202 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: c 324 THR cc_start: 0.8307 (p) cc_final: 0.8095 (p) REVERT: c 465 LYS cc_start: 0.8401 (tmtt) cc_final: 0.7563 (tttm) REVERT: c 498 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7670 (mtpt) REVERT: E 89 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8348 (tm-30) outliers start: 56 outliers final: 21 residues processed: 225 average time/residue: 1.3050 time to fit residues: 325.5684 Evaluate side-chains 197 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 202 GLN Chi-restraints excluded: chain a residue 384 VAL 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 188 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.164248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130468 restraints weight = 16425.711| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.03 r_work: 0.3266 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16125 Z= 0.142 Angle : 0.499 8.222 21915 Z= 0.263 Chirality : 0.043 0.150 2574 Planarity : 0.004 0.043 2757 Dihedral : 5.085 53.806 2250 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.99 % Allowed : 13.43 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2016 helix: 2.41 (0.27), residues: 372 sheet: 0.76 (0.20), residues: 675 loop : 0.04 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 36 HIS 0.005 0.001 HIS a 317 PHE 0.009 0.001 PHE b 137 TYR 0.017 0.002 TYR H 100E ARG 0.002 0.000 ARG c 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 0.74912 ( 9) hydrogen bonds : bond 0.03661 ( 732) hydrogen bonds : angle 5.14709 ( 1953) SS BOND : bond 0.00293 ( 27) SS BOND : angle 0.77016 ( 54) covalent geometry : bond 0.00336 (16095) covalent geometry : angle 0.49777 (21852) *********************** 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 233 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7742 (ttmt) REVERT: a 324 THR cc_start: 0.8450 (p) cc_final: 0.8089 (p) REVERT: B 87 LYS cc_start: 0.8123 (ttpp) cc_final: 0.7686 (ttmt) REVERT: b 165 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7443 (m-40) REVERT: b 429 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7692 (mtp180) REVERT: b 465 LYS cc_start: 0.8297 (tmtt) cc_final: 0.7518 (tttm) REVERT: C 77 LYS cc_start: 0.8026 (mttm) cc_final: 0.7627 (mmtt) REVERT: C 87 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7870 (ttpt) REVERT: c 202 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7315 (mt0) REVERT: c 465 LYS cc_start: 0.8422 (tmtt) cc_final: 0.7586 (tttm) REVERT: D 46 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: F 46 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: F 69 MET cc_start: 0.8748 (mtt) cc_final: 0.8461 (mtm) REVERT: G 89 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: H 46 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6602 (tm-30) outliers start: 54 outliers final: 32 residues processed: 214 average time/residue: 1.2154 time to fit residues: 287.7505 Evaluate side-chains 212 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 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 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 193 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 47 optimal weight: 0.0070 chunk 123 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.165912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132169 restraints weight = 16417.135| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.00 r_work: 0.3297 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16125 Z= 0.109 Angle : 0.462 7.753 21915 Z= 0.243 Chirality : 0.042 0.143 2574 Planarity : 0.003 0.038 2757 Dihedral : 4.921 53.550 2250 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.99 % Allowed : 14.37 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 2016 helix: 2.63 (0.27), residues: 372 sheet: 0.80 (0.20), residues: 675 loop : 0.00 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 36 HIS 0.004 0.001 HIS a 317 PHE 0.007 0.001 PHE b 137 TYR 0.013 0.001 TYR b 457 ARG 0.002 0.000 ARG G 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 3) link_NAG-ASN : angle 0.79621 ( 9) hydrogen bonds : bond 0.03190 ( 732) hydrogen bonds : angle 4.93088 ( 1953) SS BOND : bond 0.00204 ( 27) SS BOND : angle 0.59212 ( 54) covalent geometry : bond 0.00250 (16095) covalent geometry : angle 0.46149 (21852) *********************** 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 233 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7777 (ttmt) REVERT: a 202 GLN cc_start: 0.7956 (mt0) cc_final: 0.7685 (mt0) REVERT: a 324 THR cc_start: 0.8442 (p) cc_final: 0.8078 (p) REVERT: B 77 LYS cc_start: 0.8097 (mttm) cc_final: 0.7598 (mmtt) REVERT: B 87 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7706 (ttmt) REVERT: b 289 MET cc_start: 0.8295 (tpt) cc_final: 0.8034 (tpt) REVERT: b 294 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7568 (mt-10) REVERT: b 429 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7587 (mtp180) REVERT: b 465 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7531 (tttm) REVERT: b 498 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7433 (mtpt) REVERT: C 87 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7962 (ttpt) REVERT: c 185 VAL cc_start: 0.7577 (t) cc_final: 0.7278 (p) REVERT: c 202 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7432 (mt0) REVERT: c 465 LYS cc_start: 0.8415 (tmtt) cc_final: 0.7618 (tttm) REVERT: D 46 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: E 61 ARG cc_start: 0.7451 (ptt-90) cc_final: 0.7195 (ptt-90) REVERT: E 89 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: F 69 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8472 (mtm) REVERT: G 61 ARG cc_start: 0.7199 (ptt-90) cc_final: 0.6989 (ptt-90) REVERT: G 89 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8160 (pt0) outliers start: 54 outliers final: 36 residues processed: 222 average time/residue: 1.2724 time to fit residues: 313.3694 Evaluate side-chains 213 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 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 190 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 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 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 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 87 THR Chi-restraints excluded: chain F residue 108 THR 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 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 176 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 188 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 G 55 GLN I 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.160585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125262 restraints weight = 16673.335| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.18 r_work: 0.3166 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.006 0.045 16125 Z= 0.248 Angle : 0.588 9.313 21915 Z= 0.309 Chirality : 0.047 0.147 2574 Planarity : 0.004 0.045 2757 Dihedral : 5.439 54.425 2250 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.31 % Allowed : 13.88 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 2016 helix: 2.24 (0.27), residues: 372 sheet: 0.73 (0.21), residues: 621 loop : -0.33 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 36 HIS 0.007 0.002 HIS a 317 PHE 0.013 0.002 PHE b 137 TYR 0.021 0.002 TYR c 457 ARG 0.004 0.001 ARG A 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 0.84542 ( 9) hydrogen bonds : bond 0.04429 ( 732) hydrogen bonds : angle 5.39990 ( 1953) SS BOND : bond 0.00473 ( 27) SS BOND : angle 1.07230 ( 54) covalent geometry : bond 0.00603 (16095) covalent geometry : angle 0.58665 (21852) *********************** 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 254 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 176 time to evaluate : 1.683 Fit side-chains REVERT: A 87 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7970 (ttmt) REVERT: B 87 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7823 (ttmt) REVERT: b 180 SER cc_start: 0.8912 (p) cc_final: 0.8608 (p) REVERT: b 429 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7667 (mtm110) REVERT: b 465 LYS cc_start: 0.8457 (tmtt) cc_final: 0.7750 (tttm) REVERT: b 498 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7752 (mtpt) REVERT: C 77 LYS cc_start: 0.8372 (mttm) cc_final: 0.7926 (mmtt) REVERT: C 87 LYS cc_start: 0.8354 (ttpp) cc_final: 0.8086 (ttpt) REVERT: c 202 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: c 297 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8074 (tp) REVERT: c 465 LYS cc_start: 0.8521 (tmtt) cc_final: 0.7781 (tttm) REVERT: c 498 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7789 (mtpt) REVERT: D 46 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: D 96 ARG cc_start: 0.7983 (ptt-90) cc_final: 0.7712 (ptm-80) REVERT: E 89 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: F 46 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: F 69 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8582 (mtm) REVERT: F 81 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: G 89 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: H 46 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6721 (tm-30) outliers start: 78 outliers final: 51 residues processed: 230 average time/residue: 1.2815 time to fit residues: 325.9583 Evaluate side-chains 236 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain b residue 190 SER 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 67 ILE 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 128 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 159 optimal weight: 0.0050 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 98 GLN E 55 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 = 0.3836 r_free = 0.3836 target = 0.163982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130112 restraints weight = 16482.844| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.01 r_work: 0.3266 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16125 Z= 0.126 Angle : 0.483 9.530 21915 Z= 0.254 Chirality : 0.043 0.149 2574 Planarity : 0.004 0.049 2757 Dihedral : 5.091 53.759 2250 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.43 % Allowed : 15.26 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 2016 helix: 2.50 (0.27), residues: 372 sheet: 0.59 (0.20), residues: 675 loop : -0.15 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.004 0.001 HIS a 317 PHE 0.009 0.001 PHE b 137 TYR 0.014 0.001 TYR a 457 ARG 0.001 0.000 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 3) link_NAG-ASN : angle 0.82031 ( 9) hydrogen bonds : bond 0.03401 ( 732) hydrogen bonds : angle 5.05018 ( 1953) SS BOND : bond 0.00231 ( 27) SS BOND : angle 0.72529 ( 54) covalent geometry : bond 0.00296 (16095) covalent geometry : angle 0.48232 (21852) *********************** 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 243 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 1.650 Fit side-chains REVERT: A 87 LYS cc_start: 0.8273 (ttpp) cc_final: 0.7716 (ttmt) REVERT: a 202 GLN cc_start: 0.7971 (mt0) cc_final: 0.7589 (mt0) REVERT: B 87 LYS cc_start: 0.8112 (ttpp) cc_final: 0.7636 (ttmt) REVERT: b 180 SER cc_start: 0.8812 (p) cc_final: 0.8534 (p) REVERT: b 429 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7511 (mtm110) REVERT: b 465 LYS cc_start: 0.8274 (tmtt) cc_final: 0.7514 (tttm) REVERT: b 498 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7442 (mtpt) REVERT: C 77 LYS cc_start: 0.8082 (mttm) cc_final: 0.7670 (mmtt) REVERT: C 87 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7900 (ttpt) REVERT: c 297 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8024 (tp) REVERT: c 465 LYS cc_start: 0.8368 (tmtt) cc_final: 0.7569 (tttm) REVERT: c 498 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7477 (mtpt) REVERT: D 46 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: D 96 ARG cc_start: 0.7720 (ptt-90) cc_final: 0.7400 (ptm-80) REVERT: E 89 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: F 46 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6574 (tm-30) REVERT: F 69 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: G 61 ARG cc_start: 0.7022 (ptt-90) cc_final: 0.6749 (ptt-90) REVERT: G 89 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: H 46 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6520 (tm-30) outliers start: 62 outliers final: 45 residues processed: 228 average time/residue: 1.2961 time to fit residues: 327.1959 Evaluate side-chains 224 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 1.923 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 46 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 52 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: B 98 GLN C 34 GLN C 98 GLN D 58 ASN E 55 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 = 0.3836 r_free = 0.3836 target = 0.163973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130090 restraints weight = 16453.959| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.01 r_work: 0.3264 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16125 Z= 0.131 Angle : 0.486 10.218 21915 Z= 0.255 Chirality : 0.043 0.149 2574 Planarity : 0.004 0.050 2757 Dihedral : 5.063 54.097 2250 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.87 % Allowed : 15.15 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2016 helix: 2.59 (0.27), residues: 372 sheet: 0.64 (0.20), residues: 672 loop : -0.19 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS a 317 PHE 0.009 0.001 PHE b 137 TYR 0.015 0.001 TYR a 457 ARG 0.001 0.000 ARG A 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 3) link_NAG-ASN : angle 0.81146 ( 9) hydrogen bonds : bond 0.03400 ( 732) hydrogen bonds : angle 5.00623 ( 1953) SS BOND : bond 0.00246 ( 27) SS BOND : angle 0.71932 ( 54) covalent geometry : bond 0.00307 (16095) covalent geometry : angle 0.48496 (21852) *********************** 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 244 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 174 time to evaluate : 1.820 Fit side-chains REVERT: A 87 LYS cc_start: 0.8313 (ttpp) cc_final: 0.7746 (ttmt) REVERT: a 202 GLN cc_start: 0.7974 (mt0) cc_final: 0.7593 (mt0) REVERT: a 294 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7771 (mt-10) REVERT: B 87 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7679 (ttmt) REVERT: b 180 SER cc_start: 0.8815 (p) cc_final: 0.8537 (p) REVERT: b 294 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7524 (mt-10) REVERT: b 429 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7546 (mtm110) REVERT: b 465 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7545 (tttm) REVERT: b 498 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7479 (mtpt) REVERT: C 77 LYS cc_start: 0.8087 (mttm) cc_final: 0.7664 (mmtt) REVERT: C 87 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7912 (ttpt) REVERT: c 202 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: c 297 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8049 (tp) REVERT: c 465 LYS cc_start: 0.8394 (tmtt) cc_final: 0.7607 (tttm) REVERT: c 498 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7519 (mtpt) REVERT: D 46 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: D 96 ARG cc_start: 0.7747 (ptt-90) cc_final: 0.7439 (ptm-80) REVERT: F 46 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6604 (tm-30) REVERT: F 69 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: F 81 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: G 89 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: H 46 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6519 (tm-30) outliers start: 70 outliers final: 49 residues processed: 226 average time/residue: 1.2300 time to fit residues: 308.3783 Evaluate side-chains 228 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 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 202 GLN Chi-restraints excluded: chain c residue 212 CYS 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 13 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 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 = 0.3796 r_free = 0.3796 target = 0.159975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126308 restraints weight = 16572.751| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.12 r_work: 0.3187 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16125 Z= 0.301 Angle : 0.633 10.881 21915 Z= 0.332 Chirality : 0.048 0.148 2574 Planarity : 0.005 0.051 2757 Dihedral : 5.520 55.104 2247 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.15 % Allowed : 14.98 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 2016 helix: 2.10 (0.27), residues: 372 sheet: 0.59 (0.21), residues: 621 loop : -0.53 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 36 HIS 0.007 0.002 HIS a 317 PHE 0.016 0.002 PHE b 137 TYR 0.023 0.002 TYR c 457 ARG 0.005 0.001 ARG A 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 3) link_NAG-ASN : angle 1.00996 ( 9) hydrogen bonds : bond 0.04713 ( 732) hydrogen bonds : angle 5.49871 ( 1953) SS BOND : bond 0.00564 ( 27) SS BOND : angle 1.13579 ( 54) covalent geometry : bond 0.00737 (16095) covalent geometry : angle 0.63080 (21852) *********************** 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 248 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 173 time to evaluate : 1.884 Fit side-chains REVERT: A 87 LYS cc_start: 0.8462 (ttpp) cc_final: 0.7927 (ttmt) REVERT: b 180 SER cc_start: 0.8862 (p) cc_final: 0.8574 (p) REVERT: b 272 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7448 (tttm) REVERT: b 429 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7726 (mtp180) REVERT: b 465 LYS cc_start: 0.8444 (tmtt) cc_final: 0.7779 (tttm) REVERT: b 498 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7748 (mtpt) REVERT: C 87 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8121 (ttpt) REVERT: c 202 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: c 297 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8071 (tp) REVERT: c 396 MET cc_start: 0.9037 (ptp) cc_final: 0.8763 (ptm) REVERT: c 465 LYS cc_start: 0.8437 (tmtt) cc_final: 0.7761 (tttm) REVERT: c 498 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7815 (mtpt) REVERT: D 46 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: D 96 ARG cc_start: 0.8044 (ptt-90) cc_final: 0.7773 (ptm-80) REVERT: F 46 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6722 (tm-30) REVERT: F 69 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8597 (mtm) REVERT: F 81 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6386 (tm-30) REVERT: G 89 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8424 (pt0) REVERT: H 46 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6779 (tm-30) outliers start: 75 outliers final: 54 residues processed: 223 average time/residue: 1.2947 time to fit residues: 319.4743 Evaluate side-chains 235 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 170 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 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 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 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 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 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 161 optimal weight: 0.0020 chunk 151 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 193 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130200 restraints weight = 16407.161| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.00 r_work: 0.3269 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1849 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= 0.120 Angle : 0.485 11.313 21915 Z= 0.255 Chirality : 0.042 0.148 2574 Planarity : 0.004 0.052 2757 Dihedral : 5.025 53.729 2247 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.32 % Allowed : 15.92 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 2016 helix: 2.47 (0.27), residues: 372 sheet: 0.54 (0.20), residues: 675 loop : -0.29 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS a 317 PHE 0.008 0.001 PHE b 137 TYR 0.014 0.001 TYR a 457 ARG 0.002 0.000 ARG c 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 3) link_NAG-ASN : angle 0.85767 ( 9) hydrogen bonds : bond 0.03344 ( 732) hydrogen bonds : angle 5.05061 ( 1953) SS BOND : bond 0.00220 ( 27) SS BOND : angle 0.69466 ( 54) covalent geometry : bond 0.00278 (16095) covalent geometry : angle 0.48392 (21852) *********************** 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 239 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8299 (ttpp) cc_final: 0.7705 (ttmt) REVERT: a 202 GLN cc_start: 0.7933 (mt0) cc_final: 0.7645 (mt0) REVERT: b 180 SER cc_start: 0.8844 (p) cc_final: 0.8541 (p) REVERT: b 225 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7675 (mm110) REVERT: b 294 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7588 (mt-10) REVERT: b 429 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7617 (mtp180) REVERT: b 465 LYS cc_start: 0.8282 (tmtt) cc_final: 0.7514 (tttm) REVERT: b 498 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7424 (mtpt) REVERT: C 87 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7905 (ttpt) REVERT: c 200 ASP cc_start: 0.8314 (m-30) cc_final: 0.8109 (m-30) REVERT: c 202 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: c 429 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7684 (mtp180) REVERT: c 465 LYS cc_start: 0.8352 (tmtt) cc_final: 0.7561 (tttm) REVERT: c 498 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7467 (mtpt) REVERT: D 46 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: D 96 ARG cc_start: 0.7722 (ptt-90) cc_final: 0.7392 (ptm-80) REVERT: E 89 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: F 46 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6545 (tm-30) REVERT: F 69 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8502 (mtm) REVERT: F 81 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6205 (tm-30) REVERT: G 89 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8223 (pt0) REVERT: H 46 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6527 (tm-30) outliers start: 60 outliers final: 46 residues processed: 225 average time/residue: 1.3566 time to fit residues: 343.5166 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 : 1.692 ------------------------------------------------------------------------------- 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 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 202 GLN 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 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 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 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 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 181 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 58 optimal weight: 0.0570 chunk 56 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 I 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130838 restraints weight = 16503.807| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.06 r_work: 0.3272 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16125 Z= 0.114 Angle : 0.479 11.829 21915 Z= 0.251 Chirality : 0.042 0.146 2574 Planarity : 0.004 0.052 2757 Dihedral : 4.928 54.101 2247 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.15 % Allowed : 16.09 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 2016 helix: 2.63 (0.27), residues: 372 sheet: 0.61 (0.20), residues: 675 loop : -0.25 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS a 317 PHE 0.008 0.001 PHE b 137 TYR 0.013 0.001 TYR a 457 ARG 0.003 0.000 ARG G 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 3) link_NAG-ASN : angle 0.81995 ( 9) hydrogen bonds : bond 0.03227 ( 732) hydrogen bonds : angle 4.93085 ( 1953) SS BOND : bond 0.00214 ( 27) SS BOND : angle 0.67554 ( 54) covalent geometry : bond 0.00264 (16095) covalent geometry : angle 0.47847 (21852) ********************** 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 236 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 1.836 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8924 (tt0) cc_final: 0.8587 (tt0) REVERT: A 87 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7819 (ttmt) REVERT: a 202 GLN cc_start: 0.7897 (mt0) cc_final: 0.7604 (mt0) REVERT: B 77 LYS cc_start: 0.8125 (mttm) cc_final: 0.7556 (mmtt) REVERT: b 180 SER cc_start: 0.8852 (p) cc_final: 0.8555 (p) REVERT: b 294 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7521 (mt-10) REVERT: b 429 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7687 (mtp180) REVERT: b 465 LYS cc_start: 0.8331 (tmtt) cc_final: 0.7619 (tttm) REVERT: b 498 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7616 (mtpt) REVERT: C 87 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7978 (ttpt) REVERT: c 202 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: c 429 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7750 (mtp180) REVERT: c 465 LYS cc_start: 0.8409 (tmtt) cc_final: 0.7677 (tttm) REVERT: c 498 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7655 (mtpt) REVERT: D 46 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: D 96 ARG cc_start: 0.7721 (ptt-90) cc_final: 0.7426 (ptm-80) REVERT: E 89 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: F 46 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: F 69 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8494 (mtm) REVERT: F 81 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: F 105 GLN cc_start: 0.8716 (pm20) cc_final: 0.8492 (pm20) REVERT: G 89 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: H 46 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6576 (tm-30) outliers start: 57 outliers final: 44 residues processed: 222 average time/residue: 1.2951 time to fit residues: 317.7663 Evaluate side-chains 221 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 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 95 LEU Chi-restraints excluded: chain b residue 190 SER 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 202 GLN 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 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 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 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 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 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN b 225 GLN C 98 GLN D 58 ASN I 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.162064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127059 restraints weight = 15774.190| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.94 r_work: 0.3195 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16125 Z= 0.108 Angle : 0.475 11.899 21915 Z= 0.248 Chirality : 0.042 0.144 2574 Planarity : 0.003 0.052 2757 Dihedral : 4.859 53.759 2247 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.15 % Allowed : 16.31 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 2016 helix: 2.72 (0.27), residues: 372 sheet: 0.66 (0.20), residues: 675 loop : -0.23 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 50 HIS 0.004 0.001 HIS a 317 PHE 0.007 0.001 PHE b 137 TYR 0.013 0.001 TYR a 457 ARG 0.003 0.000 ARG G 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 0.78007 ( 9) hydrogen bonds : bond 0.03124 ( 732) hydrogen bonds : angle 4.85943 ( 1953) SS BOND : bond 0.00201 ( 27) SS BOND : angle 0.64487 ( 54) covalent geometry : bond 0.00247 (16095) covalent geometry : angle 0.47430 (21852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12520.52 seconds wall clock time: 213 minutes 43.45 seconds (12823.45 seconds total)