Starting phenix.real_space_refine on Tue Dec 31 13:30:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t7a_41089/12_2024/8t7a_41089_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t7a_41089/12_2024/8t7a_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_41089/12_2024/8t7a_41089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t7a_41089/12_2024/8t7a_41089.map" model { file = "/net/cci-nas-00/data/ceres_data/8t7a_41089/12_2024/8t7a_41089_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t7a_41089/12_2024/8t7a_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.71, per 1000 atoms: 0.68 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: 3.87 Conformation dependent library (CDL) restraints added in 2.2 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: 2.28 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: 6.26 Time building geometry restraints manager: 4.48 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.280 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.600 ------------------------------------------------------------------------------- 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 16095 Z= 0.351 Angle : 0.714 11.698 21852 Z= 0.416 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 *********************** 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 : 1.841 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: 1.3412 time to fit residues: 334.9394 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 : 1.873 ------------------------------------------------------------------------------- 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: 4.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 16095 Z= 0.220 Angle : 0.514 8.506 21852 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 *********************** 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 : 1.873 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8178 (ttpp) cc_final: 0.7690 (ttmt) REVERT: a 202 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: a 324 THR cc_start: 0.8532 (p) cc_final: 0.8160 (p) REVERT: B 87 LYS cc_start: 0.8019 (ttpp) cc_final: 0.7599 (ttmt) REVERT: b 289 MET cc_start: 0.8612 (tpt) cc_final: 0.8390 (tpt) REVERT: b 429 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7619 (mtp180) REVERT: b 465 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7488 (tttm) REVERT: C 31 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: C 77 LYS cc_start: 0.8024 (mttm) cc_final: 0.7638 (mmtt) REVERT: C 87 LYS cc_start: 0.8129 (ttpp) cc_final: 0.7827 (ttpt) REVERT: c 202 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: c 324 THR cc_start: 0.8240 (p) cc_final: 0.8014 (p) REVERT: c 465 LYS cc_start: 0.8298 (tmtt) cc_final: 0.7576 (tttm) REVERT: c 498 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7750 (mtpt) REVERT: E 89 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8490 (tm-30) outliers start: 56 outliers final: 21 residues processed: 225 average time/residue: 1.3969 time to fit residues: 347.2951 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 : 2.016 ------------------------------------------------------------------------------- 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 101 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 16095 Z= 0.448 Angle : 0.629 9.532 21852 Z= 0.330 Chirality : 0.048 0.150 2574 Planarity : 0.005 0.051 2757 Dihedral : 5.596 54.118 2250 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.59 % Allowed : 12.22 % Favored : 83.20 % 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: 0.62 (0.19), residues: 2016 helix: 1.96 (0.27), residues: 372 sheet: 0.72 (0.21), residues: 621 loop : -0.32 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 36 HIS 0.008 0.002 HIS a 317 PHE 0.014 0.002 PHE b 137 TYR 0.025 0.002 TYR H 100E ARG 0.004 0.001 ARG A 49 *********************** 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 266 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 183 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7676 (ttmt) REVERT: a 324 THR cc_start: 0.8510 (p) cc_final: 0.8192 (p) REVERT: B 87 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7552 (ttmt) REVERT: b 180 SER cc_start: 0.8894 (p) cc_final: 0.8581 (p) REVERT: b 272 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7229 (tttm) REVERT: b 429 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7567 (mtm110) REVERT: b 465 LYS cc_start: 0.8228 (tmtt) cc_final: 0.7504 (tttm) REVERT: b 498 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7498 (mtpt) REVERT: C 31 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: C 87 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7821 (ttpt) REVERT: c 202 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: c 297 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8053 (tp) REVERT: c 324 THR cc_start: 0.8193 (p) cc_final: 0.7979 (p) REVERT: c 465 LYS cc_start: 0.8301 (tmtt) cc_final: 0.7564 (tttm) REVERT: c 498 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7625 (mtpt) REVERT: D 46 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: F 46 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6483 (tm-30) REVERT: F 69 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8620 (mtm) REVERT: G 89 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8574 (pt0) REVERT: H 46 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6548 (tm-30) REVERT: I 61 ARG cc_start: 0.7685 (ptt-90) cc_final: 0.7331 (ptt-90) outliers start: 83 outliers final: 45 residues processed: 234 average time/residue: 1.3439 time to fit residues: 347.4504 Evaluate side-chains 229 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 384 VAL Chi-restraints excluded: chain a residue 396 MET 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 272 LYS Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 31 GLU 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 384 VAL Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 I 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16095 Z= 0.178 Angle : 0.481 7.929 21852 Z= 0.255 Chirality : 0.043 0.149 2574 Planarity : 0.004 0.050 2757 Dihedral : 5.116 53.480 2250 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.15 % Allowed : 14.59 % Favored : 82.26 % 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: 0.84 (0.19), residues: 2016 helix: 2.34 (0.27), residues: 372 sheet: 0.64 (0.20), residues: 675 loop : -0.14 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 36 HIS 0.004 0.001 HIS a 317 PHE 0.009 0.001 PHE b 137 TYR 0.013 0.001 TYR c 457 ARG 0.002 0.000 ARG G 61 *********************** 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 234 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 1.937 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7654 (ttmt) REVERT: a 185 VAL cc_start: 0.7919 (t) cc_final: 0.7620 (p) REVERT: a 202 GLN cc_start: 0.7965 (mt0) cc_final: 0.7713 (mt0) REVERT: B 87 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7599 (ttmt) REVERT: b 180 SER cc_start: 0.8806 (p) cc_final: 0.8511 (p) REVERT: b 289 MET cc_start: 0.8595 (tpt) cc_final: 0.7910 (tpt) REVERT: b 429 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7582 (mtm110) REVERT: b 465 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7503 (tttm) REVERT: C 77 LYS cc_start: 0.8067 (mttm) cc_final: 0.7621 (mmtt) REVERT: C 87 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7790 (ttpt) REVERT: c 324 THR cc_start: 0.7988 (p) cc_final: 0.7773 (p) REVERT: c 465 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7544 (tttm) REVERT: c 498 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7656 (mtpt) REVERT: D 46 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6791 (tm-30) REVERT: E 89 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: F 46 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: F 69 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8582 (mtm) REVERT: G 89 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: H 46 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6505 (tm-30) outliers start: 57 outliers final: 40 residues processed: 215 average time/residue: 1.3973 time to fit residues: 332.2138 Evaluate side-chains 217 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 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 b residue 410 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 266 ILE 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 D 58 ASN E 55 GLN G 55 GLN I 42 GLN I 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16095 Z= 0.331 Angle : 0.557 8.909 21852 Z= 0.293 Chirality : 0.045 0.148 2574 Planarity : 0.004 0.051 2757 Dihedral : 5.387 54.511 2250 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.26 % Allowed : 14.26 % Favored : 81.48 % 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: 0.65 (0.19), residues: 2016 helix: 2.22 (0.27), residues: 372 sheet: 0.53 (0.20), residues: 672 loop : -0.30 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 36 HIS 0.006 0.001 HIS a 317 PHE 0.012 0.001 PHE b 137 TYR 0.020 0.002 TYR c 457 ARG 0.003 0.000 ARG A 49 *********************** 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 249 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 172 time to evaluate : 1.982 Fit side-chains REVERT: A 87 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7634 (ttmt) REVERT: B 87 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7580 (ttmt) REVERT: b 165 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7718 (m110) REVERT: b 180 SER cc_start: 0.8853 (p) cc_final: 0.8541 (p) REVERT: b 429 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7579 (mtm110) REVERT: b 465 LYS cc_start: 0.8209 (tmtt) cc_final: 0.7530 (tttm) REVERT: b 498 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7467 (mtpt) REVERT: C 31 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: c 202 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: c 297 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8092 (tp) REVERT: c 324 THR cc_start: 0.8083 (p) cc_final: 0.7843 (p) REVERT: c 465 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7553 (tttm) REVERT: c 498 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7671 (mtpt) REVERT: D 46 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: F 46 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: F 69 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8624 (mtm) REVERT: G 89 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8514 (pt0) REVERT: H 46 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6523 (tm-30) outliers start: 77 outliers final: 54 residues processed: 224 average time/residue: 1.3603 time to fit residues: 337.4053 Evaluate side-chains 232 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 396 MET 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 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 31 GLU 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 266 ILE 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 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 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 65 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 42 GLN I 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16095 Z= 0.224 Angle : 0.501 9.529 21852 Z= 0.264 Chirality : 0.043 0.149 2574 Planarity : 0.004 0.052 2757 Dihedral : 5.194 54.001 2250 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.20 % Allowed : 14.81 % 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: 0.54 (0.19), residues: 2016 helix: 1.94 (0.27), residues: 396 sheet: 0.56 (0.20), residues: 654 loop : -0.41 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.005 0.001 HIS a 317 PHE 0.010 0.001 PHE b 137 TYR 0.015 0.002 TYR c 457 ARG 0.002 0.000 ARG A 49 *********************** 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 249 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 2.069 Fit side-chains REVERT: A 87 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7642 (ttmt) REVERT: B 87 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7603 (ttmt) REVERT: b 165 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7697 (m110) REVERT: b 180 SER cc_start: 0.8844 (p) cc_final: 0.8536 (p) REVERT: b 429 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7616 (mtm110) REVERT: b 465 LYS cc_start: 0.8181 (tmtt) cc_final: 0.7502 (tttm) REVERT: b 498 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7513 (mtpt) REVERT: C 31 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: C 77 LYS cc_start: 0.8091 (mttm) cc_final: 0.7595 (mmtt) REVERT: C 87 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7584 (ttmt) REVERT: c 202 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: c 297 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8069 (tp) REVERT: c 324 THR cc_start: 0.8042 (p) cc_final: 0.7817 (p) REVERT: c 465 LYS cc_start: 0.8252 (tmtt) cc_final: 0.7545 (tttm) REVERT: c 498 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7602 (mtpt) REVERT: D 46 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: F 46 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: F 69 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8614 (mtm) REVERT: G 89 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8455 (pt0) REVERT: H 46 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6497 (tm-30) REVERT: I 61 ARG cc_start: 0.7521 (ptt-90) cc_final: 0.7313 (ptt-90) outliers start: 76 outliers final: 54 residues processed: 226 average time/residue: 1.2859 time to fit residues: 323.0376 Evaluate side-chains 232 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 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 b residue 501 GLN Chi-restraints excluded: chain C residue 31 GLU 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 266 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 25 SER 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 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 187 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 I 42 GLN I 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16095 Z= 0.194 Angle : 0.485 10.239 21852 Z= 0.255 Chirality : 0.043 0.149 2574 Planarity : 0.004 0.053 2757 Dihedral : 5.100 54.053 2250 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.98 % Allowed : 15.42 % Favored : 80.60 % 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: 0.77 (0.19), residues: 2016 helix: 2.51 (0.27), residues: 372 sheet: 0.59 (0.20), residues: 672 loop : -0.30 (0.20), residues: 972 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 0.009 0.001 PHE b 137 TYR 0.015 0.001 TYR a 457 ARG 0.001 0.000 ARG c 282 *********************** 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 248 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 1.727 Fit side-chains REVERT: A 34 GLN cc_start: 0.8971 (tt0) cc_final: 0.8622 (tt0) REVERT: A 87 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7634 (ttmt) REVERT: B 87 LYS cc_start: 0.8094 (ttpp) cc_final: 0.7607 (ttmt) REVERT: b 180 SER cc_start: 0.8840 (p) cc_final: 0.8528 (p) REVERT: b 429 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7623 (mtm110) REVERT: b 465 LYS cc_start: 0.8176 (tmtt) cc_final: 0.7496 (tttm) REVERT: b 498 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7485 (mtpt) REVERT: C 31 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: C 87 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7583 (ttmt) REVERT: c 202 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: c 297 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8077 (tp) REVERT: c 465 LYS cc_start: 0.8249 (tmtt) cc_final: 0.7539 (tttm) REVERT: c 498 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7667 (mtpt) REVERT: D 46 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: E 61 ARG cc_start: 0.7857 (ptt-90) cc_final: 0.7589 (ptt-90) REVERT: E 89 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: F 69 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8609 (mtm) REVERT: G 89 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8425 (pt0) REVERT: H 46 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6482 (tm-30) outliers start: 72 outliers final: 56 residues processed: 226 average time/residue: 1.2847 time to fit residues: 321.8736 Evaluate side-chains 236 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 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 b residue 501 GLN Chi-restraints excluded: chain C residue 31 GLU 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 266 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 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 F residue 25 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 131 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 98 GLN D 58 ASN I 42 GLN I 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16095 Z= 0.297 Angle : 0.541 10.840 21852 Z= 0.284 Chirality : 0.045 0.147 2574 Planarity : 0.004 0.053 2757 Dihedral : 5.317 54.518 2250 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.15 % Allowed : 15.87 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.19), residues: 2016 helix: 2.36 (0.27), residues: 372 sheet: 0.49 (0.20), residues: 672 loop : -0.37 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 36 HIS 0.006 0.001 HIS a 317 PHE 0.011 0.001 PHE a 483 TYR 0.018 0.002 TYR c 457 ARG 0.003 0.000 ARG A 49 *********************** 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 249 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 174 time to evaluate : 2.013 Fit side-chains REVERT: A 87 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7629 (ttmt) REVERT: B 87 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7594 (ttmt) REVERT: b 180 SER cc_start: 0.8832 (p) cc_final: 0.8513 (p) REVERT: b 272 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7213 (tttm) REVERT: b 429 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7615 (mtp180) REVERT: b 465 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7519 (tttm) REVERT: b 498 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7535 (mtpt) REVERT: C 31 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: c 202 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: c 297 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8056 (tp) REVERT: c 429 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7629 (mtp180) REVERT: c 465 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7549 (tttm) REVERT: c 498 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7643 (mtpt) REVERT: D 46 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6831 (tm-30) REVERT: E 89 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: F 46 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6471 (tm-30) REVERT: F 69 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8632 (mtm) REVERT: G 89 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8495 (pt0) REVERT: H 46 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6509 (tm-30) outliers start: 75 outliers final: 56 residues processed: 223 average time/residue: 1.3599 time to fit residues: 335.5101 Evaluate side-chains 238 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 170 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 239 VAL Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 266 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 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 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 185 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 I 42 GLN I 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16095 Z= 0.260 Angle : 0.523 11.312 21852 Z= 0.274 Chirality : 0.044 0.147 2574 Planarity : 0.004 0.053 2757 Dihedral : 5.253 54.164 2250 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.09 % Allowed : 16.36 % Favored : 79.55 % 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: 0.65 (0.19), residues: 2016 helix: 2.40 (0.27), residues: 372 sheet: 0.52 (0.20), residues: 672 loop : -0.37 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.005 0.001 HIS a 317 PHE 0.010 0.001 PHE b 137 TYR 0.017 0.002 TYR a 457 ARG 0.002 0.000 ARG A 49 *********************** 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 243 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 169 time to evaluate : 1.908 Fit side-chains REVERT: A 87 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7645 (ttmt) REVERT: a 202 GLN cc_start: 0.7994 (mt0) cc_final: 0.7687 (mt0) REVERT: B 87 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7880 (ttpp) REVERT: b 180 SER cc_start: 0.8818 (p) cc_final: 0.8506 (p) REVERT: b 272 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7202 (tttm) REVERT: b 429 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7614 (mtp180) REVERT: b 465 LYS cc_start: 0.8197 (tmtt) cc_final: 0.7791 (tptm) REVERT: b 498 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7501 (mtpt) REVERT: C 31 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: C 87 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7599 (ttmt) REVERT: c 202 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: c 429 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7627 (mtp180) REVERT: c 465 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7552 (tttm) REVERT: c 498 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7596 (mtpt) REVERT: D 46 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: E 89 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: F 46 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6471 (tm-30) REVERT: F 69 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8628 (mtm) REVERT: G 89 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8481 (pt0) REVERT: H 46 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6505 (tm-30) outliers start: 74 outliers final: 57 residues processed: 219 average time/residue: 1.2935 time to fit residues: 314.3868 Evaluate side-chains 236 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 168 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain a residue 501 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 272 LYS Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 239 VAL Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 266 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 184 optimal weight: 0.0370 chunk 159 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 126 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 98 GLN I 42 GLN I 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16095 Z= 0.169 Angle : 0.478 11.720 21852 Z= 0.250 Chirality : 0.042 0.147 2574 Planarity : 0.004 0.053 2757 Dihedral : 5.035 53.831 2250 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.54 % Allowed : 16.80 % Favored : 79.66 % 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: 0.81 (0.19), residues: 2016 helix: 2.60 (0.27), residues: 372 sheet: 0.62 (0.20), residues: 672 loop : -0.30 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 ********************** 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 238 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 1.812 Fit side-chains REVERT: A 34 GLN cc_start: 0.8945 (tt0) cc_final: 0.8591 (tt0) REVERT: A 87 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7648 (ttmt) REVERT: a 202 GLN cc_start: 0.8012 (mt0) cc_final: 0.7702 (mt0) REVERT: b 180 SER cc_start: 0.8823 (p) cc_final: 0.8514 (p) REVERT: b 294 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7397 (mt-10) REVERT: b 429 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7618 (mtp180) REVERT: b 465 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7777 (tptm) REVERT: b 498 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7543 (mtpt) REVERT: C 87 LYS cc_start: 0.8114 (ttpp) cc_final: 0.7626 (mttp) REVERT: c 429 ARG cc_start: 0.7813 (mtp180) cc_final: 0.7609 (mtp180) REVERT: c 465 LYS cc_start: 0.8245 (tmtt) cc_final: 0.7558 (tttm) REVERT: D 46 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: E 89 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: F 46 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6468 (tm-30) REVERT: F 69 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8614 (mtm) REVERT: G 89 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: I 61 ARG cc_start: 0.7678 (ptt-90) cc_final: 0.7334 (ptt-90) outliers start: 64 outliers final: 53 residues processed: 221 average time/residue: 1.3167 time to fit residues: 322.4434 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 : 1.871 ------------------------------------------------------------------------------- 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 319 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 481 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 245 THR Chi-restraints excluded: chain c residue 266 ILE 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 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 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 0.0040 chunk 140 optimal weight: 7.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 98 GLN F 39 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 = 0.3814 r_free = 0.3814 target = 0.161847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128121 restraints weight = 16540.878| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.03 r_work: 0.3234 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16095 Z= 0.272 Angle : 0.532 11.732 21852 Z= 0.278 Chirality : 0.044 0.146 2574 Planarity : 0.004 0.053 2757 Dihedral : 5.258 54.405 2250 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.59 % Allowed : 16.92 % Favored : 79.49 % 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: 0.68 (0.19), residues: 2016 helix: 2.44 (0.27), residues: 372 sheet: 0.53 (0.20), residues: 672 loop : -0.35 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.005 0.001 HIS a 317 PHE 0.010 0.001 PHE b 137 TYR 0.018 0.002 TYR a 457 ARG 0.003 0.000 ARG G 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5731.95 seconds wall clock time: 104 minutes 27.89 seconds (6267.89 seconds total)