Starting phenix.real_space_refine on Fri Feb 6 00:14:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkn_48331/02_2026/9mkn_48331_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkn_48331/02_2026/9mkn_48331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mkn_48331/02_2026/9mkn_48331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkn_48331/02_2026/9mkn_48331.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkn_48331/02_2026/9mkn_48331_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkn_48331/02_2026/9mkn_48331_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 105 5.16 5 C 13272 2.51 5 N 3495 2.21 5 O 4140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21012 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 555 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'TRANS': 69} Chain: "B" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2848 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "C" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 555 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'TRANS': 69} Chain: "D" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2848 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "E" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 555 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'TRANS': 69} Chain: "F" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2848 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "I" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "J" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "M" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "N" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "S" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "T" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Time building chain proxies: 5.07, per 1000 atoms: 0.24 Number of scatterers: 21012 At special positions: 0 Unit cell: (140.883, 154.878, 128.754, 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 105 16.00 O 4140 8.00 N 3495 7.00 C 13272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 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 D 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 313 " - pdb=" SG CYS D 343 " distance=2.03 Simple disulfide: pdb=" SG CYS D 322 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 358 " - pdb=" SG CYS D 367 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 393 " distance=2.03 Simple disulfide: pdb=" SG CYS D 416 " - pdb=" SG CYS D 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS F 439 " distance=2.03 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS F 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 313 " - pdb=" SG CYS F 343 " distance=2.03 Simple disulfide: pdb=" SG CYS F 322 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 367 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 393 " distance=2.03 Simple disulfide: pdb=" SG CYS F 416 " - pdb=" SG CYS F 422 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 93 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 93 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 97 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 97 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 97 " distance=2.04 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.0 seconds 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5046 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 49 sheets defined 20.3% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 73 through 96 Processing helix chain 'B' and resid 137 through 142 removed outlier: 4.506A pdb=" N PHE B 140 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 removed outlier: 3.733A pdb=" N LEU B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 216 through 241 removed outlier: 4.507A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.773A pdb=" N SER B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 376 through 384 Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.562A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 506 Processing helix chain 'C' and resid 73 through 96 Processing helix chain 'D' and resid 137 through 142 removed outlier: 4.490A pdb=" N PHE D 140 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 142 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 removed outlier: 3.636A pdb=" N LEU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 195 through 203 Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 216 through 240 removed outlier: 4.168A pdb=" N ARG D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.749A pdb=" N SER D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN D 331 " --> pdb=" O GLU D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 376 through 384 Processing helix chain 'D' and resid 473 through 478 removed outlier: 3.530A pdb=" N TYR D 478 " --> pdb=" O ILE D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 506 Processing helix chain 'E' and resid 73 through 96 Processing helix chain 'F' and resid 137 through 142 removed outlier: 4.500A pdb=" N PHE F 140 " --> pdb=" O PHE F 137 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU F 142 " --> pdb=" O GLY F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 159 removed outlier: 3.503A pdb=" N VAL F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'F' and resid 195 through 203 Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 216 through 241 removed outlier: 4.323A pdb=" N ARG F 229 " --> pdb=" O GLN F 225 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU F 230 " --> pdb=" O LYS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 263 Processing helix chain 'F' and resid 267 through 277 Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.522A pdb=" N VAL F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 331 removed outlier: 3.764A pdb=" N SER F 330 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN F 331 " --> pdb=" O GLU F 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 327 through 331' Processing helix chain 'F' and resid 376 through 384 Processing helix chain 'F' and resid 473 through 478 removed outlier: 3.563A pdb=" N TYR F 478 " --> pdb=" O ILE F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 506 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.507A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.652A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 31 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.530A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.825A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 88 removed outlier: 3.839A pdb=" N VAL M 88 " --> pdb=" O ALA M 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 88 removed outlier: 3.846A pdb=" N VAL N 88 " --> pdb=" O ALA N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 92 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.724A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 92 Processing helix chain 'Q' and resid 104 through 108 removed outlier: 3.846A pdb=" N GLY Q 107 " --> pdb=" O ASP Q 104 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR Q 108 " --> pdb=" O ARG Q 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 104 through 108' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.731A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 92 Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.704A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 359 through 361 removed outlier: 8.099A pdb=" N VAL B 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS B 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 359 through 361 removed outlier: 8.099A pdb=" N VAL B 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 176 through 180 removed outlier: 11.026A pdb=" N SER B 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR A 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU B 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLU A 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP B 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL B 300 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N MET B 289 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN B 302 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER B 287 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.555A pdb=" N SER B 398 " --> pdb=" O CYS B 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'B' and resid 430 through 434 removed outlier: 6.827A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 359 through 361 removed outlier: 8.076A pdb=" N VAL D 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 45 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C 43 " --> pdb=" O CYS D 313 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N CYS D 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 359 through 361 removed outlier: 8.076A pdb=" N VAL D 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 45 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 176 through 180 removed outlier: 10.915A pdb=" N SER D 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR C 54 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU D 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLU C 60 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP D 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL D 300 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N MET D 289 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLN D 302 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER D 287 " --> pdb=" O GLN D 302 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 321 through 322 removed outlier: 3.562A pdb=" N SER D 398 " --> pdb=" O CYS D 333 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 404 through 407 Processing sheet with id=AB3, first strand: chain 'D' and resid 430 through 434 removed outlier: 6.856A pdb=" N ALA D 424 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR D 434 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N CYS D 422 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 359 through 361 removed outlier: 8.092A pdb=" N VAL F 365 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU E 45 " --> pdb=" O VAL F 365 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 43 " --> pdb=" O CYS F 313 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N CYS F 313 " --> pdb=" O GLY E 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 359 through 361 removed outlier: 8.092A pdb=" N VAL F 365 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU E 45 " --> pdb=" O VAL F 365 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU E 30 " --> pdb=" O LEU F 467 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL F 469 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE E 32 " --> pdb=" O VAL F 469 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 176 through 180 removed outlier: 12.115A pdb=" N TRP E 52 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N LEU F 188 " --> pdb=" O TRP E 52 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR E 54 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER F 190 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL E 56 " --> pdb=" O SER F 190 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL F 192 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N THR E 58 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP F 194 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU E 60 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL F 300 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N MET F 289 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLN F 302 " --> pdb=" O SER F 287 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER F 287 " --> pdb=" O GLN F 302 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 321 through 322 removed outlier: 3.561A pdb=" N SER F 398 " --> pdb=" O CYS F 333 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'F' and resid 430 through 434 removed outlier: 6.856A pdb=" N ALA F 424 " --> pdb=" O ILE F 432 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR F 434 " --> pdb=" O CYS F 422 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N CYS F 422 " --> pdb=" O THR F 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.550A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.433A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.530A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.399A pdb=" N GLU I 10 " --> pdb=" O THR I 118 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.550A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.361A pdb=" N GLU J 10 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.984A pdb=" N PHE L 76 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP L 75 " --> pdb=" O SER L 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.385A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR L 107 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.902A pdb=" N PHE M 76 " --> pdb=" O CYS M 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP M 75 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.394A pdb=" N LEU M 11 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR M 107 " --> pdb=" O TYR M 91 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY M 89 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP M 40 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.607A pdb=" N PHE N 76 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP N 75 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.482A pdb=" N LEU N 11 " --> pdb=" O GLU N 110 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR N 107 " --> pdb=" O TYR N 91 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP N 40 " --> pdb=" O LEU N 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'O' and resid 59 through 61 removed outlier: 3.955A pdb=" N TYR O 60 " --> pdb=" O PHE O 52 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N CYS O 49 " --> pdb=" O ARG O 40 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG O 40 " --> pdb=" O CYS O 49 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY O 51 " --> pdb=" O TRP O 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP O 38 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU O 110 " --> pdb=" O TYR O 103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 59 through 61 removed outlier: 3.955A pdb=" N TYR O 60 " --> pdb=" O PHE O 52 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N CYS O 49 " --> pdb=" O ARG O 40 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG O 40 " --> pdb=" O CYS O 49 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY O 51 " --> pdb=" O TRP O 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP O 38 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 4 through 6 removed outlier: 3.516A pdb=" N VAL P 19 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR P 69 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 12 through 13 Processing sheet with id=AD9, first strand: chain 'P' and resid 53 through 54 removed outlier: 3.518A pdb=" N ALA P 50 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 53 through 54 removed outlier: 3.518A pdb=" N ALA P 50 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'Q' and resid 59 through 61 removed outlier: 3.920A pdb=" N TYR Q 60 " --> pdb=" O PHE Q 52 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS Q 49 " --> pdb=" O ARG Q 40 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG Q 40 " --> pdb=" O CYS Q 49 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY Q 51 " --> pdb=" O TRP Q 38 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY Q 35 " --> pdb=" O SER Q 100 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR Q 115 " --> pdb=" O HIS Q 99 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP Q 101 " --> pdb=" O PHE Q 113 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N PHE Q 113 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TYR Q 103 " --> pdb=" O TYR Q 111 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR Q 111 " --> pdb=" O TYR Q 103 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 59 through 61 removed outlier: 3.920A pdb=" N TYR Q 60 " --> pdb=" O PHE Q 52 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS Q 49 " --> pdb=" O ARG Q 40 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG Q 40 " --> pdb=" O CYS Q 49 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY Q 51 " --> pdb=" O TRP Q 38 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY Q 35 " --> pdb=" O SER Q 100 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 4 through 6 removed outlier: 6.217A pdb=" N THR R 69 " --> pdb=" O ALA R 25 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 12 through 13 Processing sheet with id=AE7, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.917A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR R 49 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'S' and resid 59 through 61 removed outlier: 3.974A pdb=" N TYR S 60 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N CYS S 49 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG S 40 " --> pdb=" O CYS S 49 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY S 51 " --> pdb=" O TRP S 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP S 38 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU S 110 " --> pdb=" O TYR S 103 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 59 through 61 removed outlier: 3.974A pdb=" N TYR S 60 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N CYS S 49 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG S 40 " --> pdb=" O CYS S 49 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY S 51 " --> pdb=" O TRP S 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP S 38 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 4 through 6 removed outlier: 6.224A pdb=" N THR T 69 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 12 through 13 Processing sheet with id=AF4, first strand: chain 'T' and resid 53 through 54 removed outlier: 6.898A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR T 49 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) 956 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6735 1.34 - 1.46: 4728 1.46 - 1.58: 9822 1.58 - 1.70: 0 1.70 - 1.82: 141 Bond restraints: 21426 Sorted by residual: bond pdb=" CB ILE D 261 " pdb=" CG1 ILE D 261 " ideal model delta sigma weight residual 1.530 1.504 0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.50e+00 bond pdb=" C SER N 7 " pdb=" N PRO N 8 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.41e+00 bond pdb=" CA ASP S 88 " pdb=" C ASP S 88 " ideal model delta sigma weight residual 1.524 1.510 0.013 1.18e-02 7.18e+03 1.30e+00 bond pdb=" CB ASP I 99 " pdb=" CG ASP I 99 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.25e+00 ... (remaining 21421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 28899 2.83 - 5.65: 185 5.65 - 8.48: 25 8.48 - 11.31: 4 11.31 - 14.14: 2 Bond angle restraints: 29115 Sorted by residual: angle pdb=" C MET Q 87 " pdb=" N ASP Q 88 " pdb=" CA ASP Q 88 " ideal model delta sigma weight residual 121.95 135.16 -13.21 3.74e+00 7.15e-02 1.25e+01 angle pdb=" N GLY L 34 " pdb=" CA GLY L 34 " pdb=" C GLY L 34 " ideal model delta sigma weight residual 113.18 121.07 -7.89 2.37e+00 1.78e-01 1.11e+01 angle pdb=" CB MET M 94 " pdb=" CG MET M 94 " pdb=" SD MET M 94 " ideal model delta sigma weight residual 112.70 121.89 -9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" N GLY M 34 " pdb=" CA GLY M 34 " pdb=" C GLY M 34 " ideal model delta sigma weight residual 113.18 120.44 -7.26 2.37e+00 1.78e-01 9.37e+00 angle pdb=" N GLY J 114 " pdb=" CA GLY J 114 " pdb=" C GLY J 114 " ideal model delta sigma weight residual 112.08 115.16 -3.08 1.01e+00 9.80e-01 9.32e+00 ... (remaining 29110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11838 18.00 - 36.00: 861 36.00 - 54.00: 150 54.00 - 72.00: 37 72.00 - 90.00: 20 Dihedral angle restraints: 12906 sinusoidal: 5025 harmonic: 7881 Sorted by residual: dihedral pdb=" CB CYS C 69 " pdb=" SG CYS C 69 " pdb=" SG CYS D 212 " pdb=" CB CYS D 212 " ideal model delta sinusoidal sigma weight residual 93.00 169.29 -76.29 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS E 69 " pdb=" SG CYS E 69 " pdb=" SG CYS F 212 " pdb=" CB CYS F 212 " ideal model delta sinusoidal sigma weight residual 93.00 169.07 -76.07 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual 93.00 168.88 -75.88 1 1.00e+01 1.00e-02 7.26e+01 ... (remaining 12903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2863 0.065 - 0.130: 456 0.130 - 0.194: 33 0.194 - 0.259: 2 0.259 - 0.324: 3 Chirality restraints: 3357 Sorted by residual: chirality pdb=" CB ILE D 292 " pdb=" CA ILE D 292 " pdb=" CG1 ILE D 292 " pdb=" CG2 ILE D 292 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CB ILE F 292 " pdb=" CA ILE F 292 " pdb=" CG1 ILE F 292 " pdb=" CG2 ILE F 292 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE B 292 " pdb=" CA ILE B 292 " pdb=" CG1 ILE B 292 " pdb=" CG2 ILE B 292 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 3354 not shown) Planarity restraints: 3699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP O 88 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO O 89 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO O 89 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO O 89 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Q 88 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO Q 89 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO Q 89 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO Q 89 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR O 15 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C THR O 15 " 0.033 2.00e-02 2.50e+03 pdb=" O THR O 15 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN O 16 " -0.011 2.00e-02 2.50e+03 ... (remaining 3696 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 11376 3.02 - 3.49: 20462 3.49 - 3.96: 33261 3.96 - 4.43: 37580 4.43 - 4.90: 63514 Nonbonded interactions: 166193 Sorted by model distance: nonbonded pdb=" O ASN D 227 " pdb=" ND2 ASN D 227 " model vdw 2.554 3.120 nonbonded pdb=" O ASN F 227 " pdb=" ND2 ASN F 227 " model vdw 2.561 3.120 nonbonded pdb=" N ALA R 50 " pdb=" O ALA R 50 " model vdw 2.577 2.496 nonbonded pdb=" N ALA P 50 " pdb=" O ALA P 50 " model vdw 2.579 2.496 nonbonded pdb=" N ALA T 50 " pdb=" O ALA T 50 " model vdw 2.584 2.496 ... (remaining 166188 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.870 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21459 Z= 0.149 Angle : 0.654 14.137 29181 Z= 0.338 Chirality : 0.047 0.324 3357 Planarity : 0.004 0.053 3699 Dihedral : 13.341 89.995 7761 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 2682 helix: 0.08 (0.24), residues: 414 sheet: -0.15 (0.17), residues: 858 loop : -0.53 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 67 TYR 0.027 0.002 TYR H 27 PHE 0.011 0.002 PHE D 223 TRP 0.018 0.002 TRP I 50 HIS 0.004 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00327 (21426) covalent geometry : angle 0.65365 (29115) SS BOND : bond 0.00191 ( 33) SS BOND : angle 0.79056 ( 66) hydrogen bonds : bond 0.21476 ( 901) hydrogen bonds : angle 8.86951 ( 2427) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 SER cc_start: 0.8267 (t) cc_final: 0.7943 (p) REVERT: B 222 GLU cc_start: 0.7105 (tp30) cc_final: 0.6547 (tp30) REVERT: B 223 PHE cc_start: 0.7040 (t80) cc_final: 0.6803 (t80) REVERT: B 228 ASN cc_start: 0.7866 (t0) cc_final: 0.7353 (t0) REVERT: B 256 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6720 (mt-10) REVERT: B 263 ASP cc_start: 0.7688 (m-30) cc_final: 0.7422 (m-30) REVERT: B 270 GLN cc_start: 0.7800 (mt0) cc_final: 0.7516 (mt0) REVERT: B 338 ASP cc_start: 0.7010 (p0) cc_final: 0.6778 (p0) REVERT: B 448 ASP cc_start: 0.7174 (m-30) cc_final: 0.6893 (m-30) REVERT: B 477 PHE cc_start: 0.7394 (m-80) cc_final: 0.7185 (m-80) REVERT: B 487 GLU cc_start: 0.6876 (mp0) cc_final: 0.6191 (mp0) REVERT: C 44 TYR cc_start: 0.8391 (m-80) cc_final: 0.7934 (m-80) REVERT: D 168 LYS cc_start: 0.8486 (mtpp) cc_final: 0.7946 (mtmt) REVERT: D 190 SER cc_start: 0.8144 (t) cc_final: 0.7624 (p) REVERT: D 198 TYR cc_start: 0.7912 (t80) cc_final: 0.7699 (t80) REVERT: D 224 GLN cc_start: 0.7574 (mt0) cc_final: 0.7282 (mt0) REVERT: D 228 ASN cc_start: 0.7730 (t0) cc_final: 0.7251 (t0) REVERT: D 240 ASN cc_start: 0.7958 (m-40) cc_final: 0.7747 (m-40) REVERT: D 270 GLN cc_start: 0.7587 (mt0) cc_final: 0.7058 (mt0) REVERT: D 294 GLU cc_start: 0.7448 (tt0) cc_final: 0.7097 (tt0) REVERT: D 319 SER cc_start: 0.8211 (t) cc_final: 0.7976 (p) REVERT: F 263 ASP cc_start: 0.7416 (m-30) cc_final: 0.7204 (m-30) REVERT: F 319 SER cc_start: 0.8205 (t) cc_final: 0.7897 (p) REVERT: F 322 CYS cc_start: 0.5559 (m) cc_final: 0.5143 (m) REVERT: F 392 ASP cc_start: 0.7037 (p0) cc_final: 0.6805 (p0) REVERT: F 441 TYR cc_start: 0.8262 (t80) cc_final: 0.7645 (t80) REVERT: F 470 LYS cc_start: 0.7402 (mtpp) cc_final: 0.7165 (mtpp) REVERT: H 77 ASN cc_start: 0.7910 (t0) cc_final: 0.7567 (t0) REVERT: I 77 ASN cc_start: 0.8296 (t0) cc_final: 0.7901 (t0) REVERT: J 34 VAL cc_start: 0.8672 (t) cc_final: 0.8283 (p) REVERT: J 47 TRP cc_start: 0.8340 (t60) cc_final: 0.7354 (t60) REVERT: J 70 MET cc_start: 0.6768 (mpp) cc_final: 0.6511 (mtt) REVERT: J 77 ASN cc_start: 0.8429 (t0) cc_final: 0.8005 (t0) REVERT: L 28 SER cc_start: 0.6688 (t) cc_final: 0.6447 (p) REVERT: L 63 VAL cc_start: 0.6850 (t) cc_final: 0.6603 (p) REVERT: L 94 MET cc_start: 0.7166 (tmm) cc_final: 0.6917 (tmm) REVERT: M 103 PHE cc_start: 0.7586 (m-80) cc_final: 0.7362 (m-80) REVERT: R 48 ILE cc_start: 0.7756 (mm) cc_final: 0.7531 (mm) REVERT: R 67 SER cc_start: 0.8490 (p) cc_final: 0.8228 (p) REVERT: R 90 GLN cc_start: 0.7092 (pp30) cc_final: 0.6878 (tm-30) REVERT: T 3 ARG cc_start: 0.6290 (ttp80) cc_final: 0.6008 (ttp80) REVERT: T 32 TYR cc_start: 0.6952 (m-80) cc_final: 0.6401 (m-80) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.1491 time to fit residues: 112.7651 Evaluate side-chains 462 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN B 363 ASN B 494 GLN D 225 GLN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN D 363 ASN ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN H 65 GLN H 85 ASN I 65 GLN J 65 GLN J 85 ASN P 38 GLN ** T 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.150505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128104 restraints weight = 31561.423| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.40 r_work: 0.3529 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21459 Z= 0.232 Angle : 0.627 13.168 29181 Z= 0.332 Chirality : 0.046 0.234 3357 Planarity : 0.005 0.050 3699 Dihedral : 4.794 35.341 2934 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.54 % Allowed : 9.60 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2682 helix: 0.99 (0.25), residues: 390 sheet: 0.21 (0.17), residues: 927 loop : -0.32 (0.18), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 66 TYR 0.023 0.002 TYR D 342 PHE 0.016 0.002 PHE F 351 TRP 0.023 0.002 TRP J 47 HIS 0.005 0.002 HIS D 159 Details of bonding type rmsd covalent geometry : bond 0.00513 (21426) covalent geometry : angle 0.62604 (29115) SS BOND : bond 0.00378 ( 33) SS BOND : angle 0.97637 ( 66) hydrogen bonds : bond 0.04383 ( 901) hydrogen bonds : angle 6.48238 ( 2427) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 493 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 SER cc_start: 0.8596 (t) cc_final: 0.8226 (p) REVERT: B 256 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 259 SER cc_start: 0.8308 (t) cc_final: 0.7887 (p) REVERT: B 284 GLN cc_start: 0.7894 (mt0) cc_final: 0.7612 (mt0) REVERT: B 338 ASP cc_start: 0.8104 (p0) cc_final: 0.7557 (p0) REVERT: B 425 SER cc_start: 0.8531 (p) cc_final: 0.8305 (t) REVERT: B 426 ASN cc_start: 0.8096 (t0) cc_final: 0.7741 (t0) REVERT: B 448 ASP cc_start: 0.7393 (m-30) cc_final: 0.7116 (m-30) REVERT: B 465 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7804 (ttpp) REVERT: B 487 GLU cc_start: 0.6687 (mp0) cc_final: 0.5760 (mp0) REVERT: C 44 TYR cc_start: 0.8639 (m-80) cc_final: 0.8040 (m-80) REVERT: C 82 GLU cc_start: 0.6960 (tp30) cc_final: 0.6732 (tp30) REVERT: D 168 LYS cc_start: 0.8415 (mtpp) cc_final: 0.7966 (mtmt) REVERT: D 175 ASN cc_start: 0.7788 (m-40) cc_final: 0.7414 (m-40) REVERT: D 180 SER cc_start: 0.8387 (m) cc_final: 0.8168 (p) REVERT: D 190 SER cc_start: 0.8592 (t) cc_final: 0.8120 (p) REVERT: D 224 GLN cc_start: 0.8280 (mt0) cc_final: 0.8021 (mt0) REVERT: D 240 ASN cc_start: 0.8177 (m-40) cc_final: 0.7883 (m-40) REVERT: D 259 SER cc_start: 0.8090 (m) cc_final: 0.7739 (p) REVERT: D 270 GLN cc_start: 0.7979 (mt0) cc_final: 0.7470 (mt0) REVERT: D 284 GLN cc_start: 0.8118 (mt0) cc_final: 0.7809 (mt0) REVERT: D 294 GLU cc_start: 0.7954 (tt0) cc_final: 0.7453 (tt0) REVERT: D 319 SER cc_start: 0.8471 (t) cc_final: 0.8057 (p) REVERT: D 338 ASP cc_start: 0.7916 (p0) cc_final: 0.7600 (p0) REVERT: D 373 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7710 (mp) REVERT: D 487 GLU cc_start: 0.6669 (mp0) cc_final: 0.5624 (mp0) REVERT: E 82 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6691 (tm-30) REVERT: F 166 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6718 (mtpt) REVERT: F 190 SER cc_start: 0.8708 (t) cc_final: 0.8314 (p) REVERT: F 227 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7943 (t0) REVERT: F 234 THR cc_start: 0.8675 (p) cc_final: 0.8443 (t) REVERT: F 256 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7271 (mt-10) REVERT: F 263 ASP cc_start: 0.7723 (m-30) cc_final: 0.7444 (m-30) REVERT: F 284 GLN cc_start: 0.7950 (mt0) cc_final: 0.7614 (mt0) REVERT: F 289 MET cc_start: 0.8411 (tpt) cc_final: 0.8172 (tpt) REVERT: F 338 ASP cc_start: 0.7906 (p0) cc_final: 0.7497 (p0) REVERT: F 441 TYR cc_start: 0.8695 (t80) cc_final: 0.8281 (t80) REVERT: F 470 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7883 (mtpp) REVERT: H 38 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7877 (ttp80) REVERT: I 77 ASN cc_start: 0.8741 (t0) cc_final: 0.8262 (t0) REVERT: I 81 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6524 (tmm) REVERT: J 23 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7702 (ttmm) REVERT: J 47 TRP cc_start: 0.8508 (t60) cc_final: 0.7793 (t60) REVERT: J 70 MET cc_start: 0.7382 (mpp) cc_final: 0.6695 (mtt) REVERT: J 77 ASN cc_start: 0.8791 (t0) cc_final: 0.8376 (t0) REVERT: J 113 GLN cc_start: 0.7850 (pm20) cc_final: 0.7638 (pm20) REVERT: L 4 MET cc_start: 0.7528 (mpp) cc_final: 0.7213 (mpp) REVERT: L 22 SER cc_start: 0.7205 (p) cc_final: 0.6918 (p) REVERT: L 63 VAL cc_start: 0.7420 (t) cc_final: 0.7191 (p) REVERT: L 94 MET cc_start: 0.7955 (tmm) cc_final: 0.7593 (tmm) REVERT: N 22 SER cc_start: 0.7621 (p) cc_final: 0.7394 (p) REVERT: O 100 SER cc_start: 0.7945 (t) cc_final: 0.7662 (p) REVERT: Q 2 VAL cc_start: 0.8007 (t) cc_final: 0.7805 (p) REVERT: R 32 TYR cc_start: 0.7761 (m-80) cc_final: 0.7491 (m-80) REVERT: R 48 ILE cc_start: 0.7849 (mm) cc_final: 0.7612 (mm) REVERT: R 90 GLN cc_start: 0.7127 (pp30) cc_final: 0.6713 (pp30) REVERT: R 100 GLN cc_start: 0.7442 (mp10) cc_final: 0.7013 (mp10) REVERT: S 2 VAL cc_start: 0.8109 (t) cc_final: 0.7884 (p) REVERT: T 32 TYR cc_start: 0.7691 (m-80) cc_final: 0.7295 (m-80) REVERT: T 100 GLN cc_start: 0.7870 (mp10) cc_final: 0.7439 (mp10) outliers start: 37 outliers final: 20 residues processed: 506 average time/residue: 0.1599 time to fit residues: 123.0703 Evaluate side-chains 499 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 475 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 227 ASN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 67 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 133 optimal weight: 0.0000 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN D 363 ASN F 224 GLN ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 270 GLN F 302 GLN I 39 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129390 restraints weight = 31499.385| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.41 r_work: 0.3516 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21459 Z= 0.159 Angle : 0.565 14.281 29181 Z= 0.294 Chirality : 0.044 0.166 3357 Planarity : 0.004 0.047 3699 Dihedral : 4.612 33.847 2934 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.84 % Allowed : 13.85 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2682 helix: 1.55 (0.26), residues: 375 sheet: 0.25 (0.17), residues: 930 loop : -0.22 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 44 TYR 0.019 0.002 TYR D 306 PHE 0.027 0.002 PHE D 223 TRP 0.016 0.002 TRP J 47 HIS 0.005 0.002 HIS Q 99 Details of bonding type rmsd covalent geometry : bond 0.00346 (21426) covalent geometry : angle 0.56362 (29115) SS BOND : bond 0.00410 ( 33) SS BOND : angle 0.90814 ( 66) hydrogen bonds : bond 0.03683 ( 901) hydrogen bonds : angle 5.94538 ( 2427) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 485 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.6882 (tp30) cc_final: 0.6544 (tp30) REVERT: A 87 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8120 (mmtp) REVERT: B 190 SER cc_start: 0.8529 (t) cc_final: 0.8185 (m) REVERT: B 227 ASN cc_start: 0.7983 (t0) cc_final: 0.7606 (t0) REVERT: B 228 ASN cc_start: 0.8132 (t0) cc_final: 0.7644 (t0) REVERT: B 259 SER cc_start: 0.8317 (t) cc_final: 0.7799 (p) REVERT: B 260 LEU cc_start: 0.8461 (tt) cc_final: 0.8209 (tp) REVERT: B 337 THR cc_start: 0.8474 (p) cc_final: 0.8242 (p) REVERT: B 338 ASP cc_start: 0.8096 (p0) cc_final: 0.7587 (p0) REVERT: B 425 SER cc_start: 0.8553 (p) cc_final: 0.8283 (t) REVERT: B 448 ASP cc_start: 0.7385 (m-30) cc_final: 0.7162 (m-30) REVERT: C 44 TYR cc_start: 0.8644 (m-80) cc_final: 0.8079 (m-80) REVERT: C 82 GLU cc_start: 0.7077 (tp30) cc_final: 0.6735 (tp30) REVERT: D 168 LYS cc_start: 0.8357 (mtpp) cc_final: 0.7961 (mtmt) REVERT: D 175 ASN cc_start: 0.7728 (m-40) cc_final: 0.7468 (m-40) REVERT: D 190 SER cc_start: 0.8549 (t) cc_final: 0.8054 (p) REVERT: D 224 GLN cc_start: 0.8235 (mt0) cc_final: 0.8009 (mt0) REVERT: D 240 ASN cc_start: 0.8135 (m-40) cc_final: 0.7840 (m-40) REVERT: D 259 SER cc_start: 0.8117 (m) cc_final: 0.7749 (p) REVERT: D 270 GLN cc_start: 0.7964 (mt0) cc_final: 0.7493 (mt0) REVERT: D 294 GLU cc_start: 0.7979 (tt0) cc_final: 0.7512 (tt0) REVERT: D 319 SER cc_start: 0.8488 (t) cc_final: 0.7504 (p) REVERT: D 338 ASP cc_start: 0.7893 (p0) cc_final: 0.7411 (p0) REVERT: D 399 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8287 (mttp) REVERT: D 487 GLU cc_start: 0.6675 (mp0) cc_final: 0.5639 (mp0) REVERT: F 190 SER cc_start: 0.8749 (t) cc_final: 0.8356 (p) REVERT: F 227 ASN cc_start: 0.8211 (t0) cc_final: 0.7934 (t0) REVERT: F 234 THR cc_start: 0.8703 (p) cc_final: 0.8466 (t) REVERT: F 256 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7296 (mt-10) REVERT: F 263 ASP cc_start: 0.7607 (m-30) cc_final: 0.7278 (m-30) REVERT: F 284 GLN cc_start: 0.8016 (mt0) cc_final: 0.7705 (mt0) REVERT: F 338 ASP cc_start: 0.7935 (p0) cc_final: 0.7493 (p0) REVERT: F 399 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8474 (mttm) REVERT: F 426 ASN cc_start: 0.8081 (t0) cc_final: 0.7781 (t0) REVERT: F 441 TYR cc_start: 0.8671 (t80) cc_final: 0.8277 (t80) REVERT: I 23 LYS cc_start: 0.7937 (tttm) cc_final: 0.7681 (ttpp) REVERT: I 70 MET cc_start: 0.7469 (mpp) cc_final: 0.6850 (mpp) REVERT: I 77 ASN cc_start: 0.8660 (t0) cc_final: 0.8246 (t0) REVERT: I 81 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6504 (tmm) REVERT: J 47 TRP cc_start: 0.8535 (t60) cc_final: 0.7910 (t60) REVERT: J 70 MET cc_start: 0.7326 (mpp) cc_final: 0.6760 (mpp) REVERT: J 77 ASN cc_start: 0.8650 (t0) cc_final: 0.8304 (t0) REVERT: J 110 TYR cc_start: 0.8063 (m-80) cc_final: 0.7706 (m-10) REVERT: L 4 MET cc_start: 0.7529 (mpp) cc_final: 0.7311 (mpp) REVERT: L 22 SER cc_start: 0.7257 (p) cc_final: 0.6961 (p) REVERT: L 94 MET cc_start: 0.7904 (tmm) cc_final: 0.7575 (tmm) REVERT: N 22 SER cc_start: 0.7617 (p) cc_final: 0.7388 (p) REVERT: N 63 VAL cc_start: 0.7450 (t) cc_final: 0.7169 (p) REVERT: N 66 ARG cc_start: 0.7222 (ttm170) cc_final: 0.6990 (ttp80) REVERT: O 100 SER cc_start: 0.7965 (t) cc_final: 0.7715 (p) REVERT: P 35 TRP cc_start: 0.7988 (m100) cc_final: 0.7422 (m100) REVERT: R 32 TYR cc_start: 0.7808 (m-80) cc_final: 0.7424 (m-80) REVERT: R 90 GLN cc_start: 0.7011 (pp30) cc_final: 0.6442 (pp30) REVERT: R 100 GLN cc_start: 0.7524 (mp10) cc_final: 0.7134 (mp10) REVERT: S 2 VAL cc_start: 0.8124 (t) cc_final: 0.7908 (p) REVERT: S 78 ASN cc_start: 0.6320 (t0) cc_final: 0.6074 (t0) REVERT: T 32 TYR cc_start: 0.7596 (m-80) cc_final: 0.7171 (m-80) REVERT: T 100 GLN cc_start: 0.7921 (mp10) cc_final: 0.7523 (mp10) outliers start: 44 outliers final: 29 residues processed: 503 average time/residue: 0.1430 time to fit residues: 110.6535 Evaluate side-chains 502 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 472 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 67 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 68 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN C 27 ASN D 175 ASN D 363 ASN E 27 ASN ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN F 302 GLN F 437 ASN I 39 GLN I 65 GLN J 65 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 GLN ** T 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126675 restraints weight = 31445.570| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.38 r_work: 0.3483 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21459 Z= 0.235 Angle : 0.618 14.301 29181 Z= 0.322 Chirality : 0.046 0.239 3357 Planarity : 0.004 0.052 3699 Dihedral : 4.850 32.002 2934 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.30 % Allowed : 14.18 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2682 helix: 1.02 (0.25), residues: 390 sheet: 0.25 (0.17), residues: 921 loop : -0.38 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 229 TYR 0.024 0.002 TYR C 86 PHE 0.024 0.002 PHE D 223 TRP 0.022 0.002 TRP J 111 HIS 0.006 0.002 HIS Q 99 Details of bonding type rmsd covalent geometry : bond 0.00520 (21426) covalent geometry : angle 0.61716 (29115) SS BOND : bond 0.00318 ( 33) SS BOND : angle 0.88558 ( 66) hydrogen bonds : bond 0.03840 ( 901) hydrogen bonds : angle 5.84485 ( 2427) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 501 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 SER cc_start: 0.8533 (t) cc_final: 0.8147 (p) REVERT: B 227 ASN cc_start: 0.7909 (t0) cc_final: 0.7524 (m110) REVERT: B 228 ASN cc_start: 0.8135 (t0) cc_final: 0.7566 (t0) REVERT: B 256 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7283 (mt-10) REVERT: B 259 SER cc_start: 0.8229 (t) cc_final: 0.7889 (p) REVERT: B 336 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7670 (ttp80) REVERT: B 338 ASP cc_start: 0.8152 (p0) cc_final: 0.7793 (p0) REVERT: B 425 SER cc_start: 0.8525 (p) cc_final: 0.8291 (t) REVERT: B 426 ASN cc_start: 0.8125 (t0) cc_final: 0.7797 (t0) REVERT: C 44 TYR cc_start: 0.8708 (m-80) cc_final: 0.8076 (m-80) REVERT: C 82 GLU cc_start: 0.7182 (tp30) cc_final: 0.6754 (tp30) REVERT: D 190 SER cc_start: 0.8618 (t) cc_final: 0.8097 (p) REVERT: D 224 GLN cc_start: 0.8255 (mt0) cc_final: 0.8038 (mt0) REVERT: D 226 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7982 (mtpt) REVERT: D 240 ASN cc_start: 0.8166 (m-40) cc_final: 0.7901 (m-40) REVERT: D 270 GLN cc_start: 0.8030 (mt0) cc_final: 0.7506 (mt0) REVERT: D 319 SER cc_start: 0.8517 (t) cc_final: 0.8040 (p) REVERT: D 338 ASP cc_start: 0.7860 (p0) cc_final: 0.7329 (p0) REVERT: D 441 TYR cc_start: 0.8692 (t80) cc_final: 0.8371 (t80) REVERT: D 487 GLU cc_start: 0.6603 (mp0) cc_final: 0.5548 (mp0) REVERT: E 82 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6806 (tm-30) REVERT: F 190 SER cc_start: 0.8778 (t) cc_final: 0.8418 (p) REVERT: F 227 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7925 (t0) REVERT: F 228 ASN cc_start: 0.8240 (t0) cc_final: 0.7949 (t0) REVERT: F 256 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7333 (mt-10) REVERT: F 263 ASP cc_start: 0.7553 (m-30) cc_final: 0.7237 (m-30) REVERT: F 284 GLN cc_start: 0.8050 (mt0) cc_final: 0.7750 (mt0) REVERT: F 338 ASP cc_start: 0.7991 (p0) cc_final: 0.7578 (p0) REVERT: F 371 ASN cc_start: 0.8170 (p0) cc_final: 0.7903 (p0) REVERT: F 399 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8495 (mttm) REVERT: F 426 ASN cc_start: 0.8065 (t0) cc_final: 0.7780 (t0) REVERT: F 441 TYR cc_start: 0.8718 (t80) cc_final: 0.8508 (t80) REVERT: H 28 SER cc_start: 0.8604 (p) cc_final: 0.8361 (p) REVERT: H 77 ASN cc_start: 0.8507 (t0) cc_final: 0.8049 (t0) REVERT: H 80 TYR cc_start: 0.6357 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: I 23 LYS cc_start: 0.7992 (tttm) cc_final: 0.7766 (ttpp) REVERT: I 70 MET cc_start: 0.7505 (mpp) cc_final: 0.6840 (mpp) REVERT: I 77 ASN cc_start: 0.8738 (t0) cc_final: 0.8281 (t0) REVERT: I 81 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6616 (tmm) REVERT: J 70 MET cc_start: 0.7395 (mpp) cc_final: 0.6985 (mpp) REVERT: J 77 ASN cc_start: 0.8698 (t0) cc_final: 0.8395 (t0) REVERT: L 4 MET cc_start: 0.7506 (mpp) cc_final: 0.7302 (mpp) REVERT: L 22 SER cc_start: 0.7372 (p) cc_final: 0.7114 (p) REVERT: L 94 MET cc_start: 0.7908 (tmm) cc_final: 0.7540 (tmm) REVERT: N 22 SER cc_start: 0.7740 (p) cc_final: 0.7458 (p) REVERT: N 63 VAL cc_start: 0.7594 (t) cc_final: 0.7350 (p) REVERT: N 66 ARG cc_start: 0.7175 (ttm170) cc_final: 0.6700 (ttm170) REVERT: O 100 SER cc_start: 0.8007 (t) cc_final: 0.7702 (p) REVERT: P 35 TRP cc_start: 0.8063 (m100) cc_final: 0.7505 (m100) REVERT: R 32 TYR cc_start: 0.7839 (m-80) cc_final: 0.7353 (m-80) REVERT: R 100 GLN cc_start: 0.7676 (mp10) cc_final: 0.7323 (mp10) REVERT: S 2 VAL cc_start: 0.8181 (t) cc_final: 0.7981 (p) REVERT: S 78 ASN cc_start: 0.6399 (t0) cc_final: 0.6120 (t0) REVERT: T 100 GLN cc_start: 0.7927 (mp10) cc_final: 0.7565 (mp10) outliers start: 79 outliers final: 54 residues processed: 533 average time/residue: 0.1360 time to fit residues: 112.2620 Evaluate side-chains 550 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 493 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 227 ASN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain J residue 113 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 227 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 129 optimal weight: 0.0570 chunk 184 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN D 317 HIS ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN ** T 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.150858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128445 restraints weight = 31447.883| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.40 r_work: 0.3517 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21459 Z= 0.142 Angle : 0.560 15.976 29181 Z= 0.288 Chirality : 0.044 0.172 3357 Planarity : 0.004 0.055 3699 Dihedral : 4.589 30.296 2934 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.88 % Allowed : 16.15 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2682 helix: 1.09 (0.26), residues: 393 sheet: 0.29 (0.17), residues: 894 loop : -0.34 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 66 TYR 0.019 0.002 TYR B 306 PHE 0.017 0.001 PHE D 223 TRP 0.018 0.001 TRP T 35 HIS 0.004 0.001 HIS Q 99 Details of bonding type rmsd covalent geometry : bond 0.00313 (21426) covalent geometry : angle 0.55853 (29115) SS BOND : bond 0.00255 ( 33) SS BOND : angle 0.92633 ( 66) hydrogen bonds : bond 0.03299 ( 901) hydrogen bonds : angle 5.59266 ( 2427) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 489 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 CYS cc_start: 0.7381 (t) cc_final: 0.7118 (t) REVERT: A 87 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8088 (mmtp) REVERT: B 190 SER cc_start: 0.8529 (t) cc_final: 0.8207 (m) REVERT: B 227 ASN cc_start: 0.7831 (t0) cc_final: 0.7395 (m110) REVERT: B 228 ASN cc_start: 0.8049 (t0) cc_final: 0.7491 (t0) REVERT: B 256 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7284 (mt-10) REVERT: B 259 SER cc_start: 0.8201 (t) cc_final: 0.7603 (p) REVERT: B 263 ASP cc_start: 0.7734 (m-30) cc_final: 0.7263 (m-30) REVERT: B 284 GLN cc_start: 0.7866 (mt0) cc_final: 0.7514 (mt0) REVERT: B 338 ASP cc_start: 0.8008 (p0) cc_final: 0.7544 (p0) REVERT: B 425 SER cc_start: 0.8526 (p) cc_final: 0.8289 (t) REVERT: C 44 TYR cc_start: 0.8676 (m-80) cc_final: 0.8074 (m-80) REVERT: C 82 GLU cc_start: 0.7156 (tp30) cc_final: 0.6689 (tp30) REVERT: D 190 SER cc_start: 0.8643 (t) cc_final: 0.8130 (p) REVERT: D 224 GLN cc_start: 0.8258 (mt0) cc_final: 0.8032 (mt0) REVERT: D 240 ASN cc_start: 0.8151 (m-40) cc_final: 0.7862 (m-40) REVERT: D 261 ILE cc_start: 0.8439 (tt) cc_final: 0.8234 (tt) REVERT: D 270 GLN cc_start: 0.7977 (mt0) cc_final: 0.7474 (mt0) REVERT: D 319 SER cc_start: 0.8498 (t) cc_final: 0.8027 (p) REVERT: D 338 ASP cc_start: 0.7753 (p0) cc_final: 0.7354 (p0) REVERT: D 399 LYS cc_start: 0.8631 (mttp) cc_final: 0.8308 (mttp) REVERT: D 487 GLU cc_start: 0.6603 (mp0) cc_final: 0.5514 (mp0) REVERT: F 190 SER cc_start: 0.8779 (t) cc_final: 0.8427 (p) REVERT: F 227 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7915 (t0) REVERT: F 228 ASN cc_start: 0.8215 (t0) cc_final: 0.7935 (t0) REVERT: F 256 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7364 (mt-10) REVERT: F 263 ASP cc_start: 0.7491 (m-30) cc_final: 0.7194 (m-30) REVERT: F 284 GLN cc_start: 0.8018 (mt0) cc_final: 0.7692 (mt0) REVERT: F 286 TYR cc_start: 0.8479 (m-80) cc_final: 0.7827 (m-80) REVERT: F 338 ASP cc_start: 0.7956 (p0) cc_final: 0.7498 (p0) REVERT: F 371 ASN cc_start: 0.8152 (p0) cc_final: 0.7918 (p0) REVERT: F 399 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8395 (mttp) REVERT: F 426 ASN cc_start: 0.8026 (t0) cc_final: 0.7745 (t0) REVERT: F 441 TYR cc_start: 0.8697 (t80) cc_final: 0.8471 (t80) REVERT: H 28 SER cc_start: 0.8564 (p) cc_final: 0.8192 (p) REVERT: H 80 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.4907 (m-80) REVERT: H 81 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6487 (tmm) REVERT: H 99 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: I 23 LYS cc_start: 0.7979 (tttm) cc_final: 0.7738 (ttpp) REVERT: I 70 MET cc_start: 0.7453 (mpp) cc_final: 0.6839 (mpp) REVERT: I 77 ASN cc_start: 0.8710 (t0) cc_final: 0.8264 (t0) REVERT: I 81 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6521 (tmm) REVERT: I 110 TYR cc_start: 0.8021 (m-10) cc_final: 0.7686 (m-10) REVERT: J 70 MET cc_start: 0.7383 (mpp) cc_final: 0.6970 (mpp) REVERT: L 22 SER cc_start: 0.7280 (p) cc_final: 0.7013 (p) REVERT: L 94 MET cc_start: 0.7861 (tmm) cc_final: 0.7492 (tmm) REVERT: N 22 SER cc_start: 0.7698 (p) cc_final: 0.7442 (p) REVERT: N 63 VAL cc_start: 0.7624 (t) cc_final: 0.7370 (p) REVERT: N 66 ARG cc_start: 0.7145 (ttm170) cc_final: 0.6706 (ttm170) REVERT: N 103 PHE cc_start: 0.8350 (m-80) cc_final: 0.8079 (m-80) REVERT: P 35 TRP cc_start: 0.8012 (m100) cc_final: 0.7428 (m100) REVERT: R 4 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7736 (t) REVERT: R 32 TYR cc_start: 0.7774 (m-80) cc_final: 0.7281 (m-80) REVERT: R 100 GLN cc_start: 0.7679 (mp10) cc_final: 0.7323 (mp10) REVERT: S 2 VAL cc_start: 0.8194 (t) cc_final: 0.7991 (p) REVERT: S 78 ASN cc_start: 0.6273 (t0) cc_final: 0.5997 (t0) REVERT: T 100 GLN cc_start: 0.7936 (mp10) cc_final: 0.7578 (mp10) outliers start: 69 outliers final: 52 residues processed: 519 average time/residue: 0.1410 time to fit residues: 113.6199 Evaluate side-chains 539 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 481 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 227 ASN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain J residue 113 GLN Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 190 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 232 optimal weight: 0.3980 chunk 139 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 258 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN C 27 ASN D 363 ASN ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN F 437 ASN L 43 GLN T 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.150857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128414 restraints weight = 31161.369| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.40 r_work: 0.3515 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21459 Z= 0.151 Angle : 0.561 16.369 29181 Z= 0.288 Chirality : 0.044 0.250 3357 Planarity : 0.004 0.055 3699 Dihedral : 4.543 32.303 2934 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.09 % Allowed : 16.56 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2682 helix: 1.09 (0.26), residues: 396 sheet: 0.34 (0.17), residues: 894 loop : -0.33 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 336 TYR 0.021 0.002 TYR F 306 PHE 0.015 0.001 PHE L 103 TRP 0.020 0.002 TRP T 35 HIS 0.004 0.001 HIS S 99 Details of bonding type rmsd covalent geometry : bond 0.00336 (21426) covalent geometry : angle 0.56012 (29115) SS BOND : bond 0.00258 ( 33) SS BOND : angle 0.84839 ( 66) hydrogen bonds : bond 0.03262 ( 901) hydrogen bonds : angle 5.47020 ( 2427) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 479 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 CYS cc_start: 0.7352 (t) cc_final: 0.7055 (t) REVERT: A 87 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8057 (mmtp) REVERT: B 190 SER cc_start: 0.8549 (t) cc_final: 0.8220 (m) REVERT: B 227 ASN cc_start: 0.7822 (t0) cc_final: 0.7427 (m110) REVERT: B 228 ASN cc_start: 0.8059 (t0) cc_final: 0.7517 (t0) REVERT: B 256 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7367 (mt-10) REVERT: B 259 SER cc_start: 0.8209 (t) cc_final: 0.7517 (p) REVERT: B 263 ASP cc_start: 0.7796 (m-30) cc_final: 0.7247 (m-30) REVERT: B 284 GLN cc_start: 0.7830 (mt0) cc_final: 0.7537 (mt0) REVERT: B 338 ASP cc_start: 0.8085 (p0) cc_final: 0.7587 (p0) REVERT: B 393 CYS cc_start: 0.6500 (m) cc_final: 0.6249 (m) REVERT: C 44 TYR cc_start: 0.8693 (m-80) cc_final: 0.8057 (m-80) REVERT: D 190 SER cc_start: 0.8662 (t) cc_final: 0.8140 (p) REVERT: D 224 GLN cc_start: 0.8295 (mt0) cc_final: 0.8071 (mt0) REVERT: D 240 ASN cc_start: 0.8113 (m-40) cc_final: 0.7830 (m-40) REVERT: D 261 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8315 (tt) REVERT: D 270 GLN cc_start: 0.8009 (mt0) cc_final: 0.7534 (mt0) REVERT: D 319 SER cc_start: 0.8513 (t) cc_final: 0.8037 (p) REVERT: D 338 ASP cc_start: 0.7766 (p0) cc_final: 0.7308 (p0) REVERT: D 399 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8277 (mttm) REVERT: D 487 GLU cc_start: 0.6541 (mp0) cc_final: 0.5470 (mp0) REVERT: F 190 SER cc_start: 0.8820 (t) cc_final: 0.8435 (p) REVERT: F 227 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7928 (t0) REVERT: F 228 ASN cc_start: 0.8226 (t0) cc_final: 0.7920 (t0) REVERT: F 263 ASP cc_start: 0.7474 (m-30) cc_final: 0.7168 (m-30) REVERT: F 284 GLN cc_start: 0.8036 (mt0) cc_final: 0.7748 (mt0) REVERT: F 286 TYR cc_start: 0.8476 (m-80) cc_final: 0.7838 (m-80) REVERT: F 338 ASP cc_start: 0.7943 (p0) cc_final: 0.7469 (p0) REVERT: F 371 ASN cc_start: 0.8189 (p0) cc_final: 0.7944 (p0) REVERT: F 399 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8419 (mttm) REVERT: F 441 TYR cc_start: 0.8687 (t80) cc_final: 0.8483 (t80) REVERT: H 28 SER cc_start: 0.8578 (p) cc_final: 0.8265 (p) REVERT: H 80 TYR cc_start: 0.6356 (OUTLIER) cc_final: 0.4953 (m-80) REVERT: H 99 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: I 23 LYS cc_start: 0.7965 (tttm) cc_final: 0.7757 (ttpp) REVERT: I 70 MET cc_start: 0.7478 (mpp) cc_final: 0.6866 (mpp) REVERT: I 77 ASN cc_start: 0.8658 (t0) cc_final: 0.8230 (t0) REVERT: I 81 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6528 (tmm) REVERT: I 110 TYR cc_start: 0.7994 (m-10) cc_final: 0.7664 (m-10) REVERT: J 70 MET cc_start: 0.7372 (mpp) cc_final: 0.6982 (mpp) REVERT: J 77 ASN cc_start: 0.8648 (t0) cc_final: 0.8257 (t0) REVERT: L 22 SER cc_start: 0.7284 (p) cc_final: 0.6999 (p) REVERT: L 94 MET cc_start: 0.7915 (tmm) cc_final: 0.7579 (tmm) REVERT: N 22 SER cc_start: 0.7709 (p) cc_final: 0.7445 (p) REVERT: N 63 VAL cc_start: 0.7645 (t) cc_final: 0.7389 (p) REVERT: N 66 ARG cc_start: 0.7108 (ttm170) cc_final: 0.6648 (ttm170) REVERT: N 103 PHE cc_start: 0.8391 (m-80) cc_final: 0.8134 (m-80) REVERT: O 87 MET cc_start: 0.6809 (mmm) cc_final: 0.4556 (ptm) REVERT: P 4 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7703 (t) REVERT: P 35 TRP cc_start: 0.8034 (m100) cc_final: 0.7444 (m100) REVERT: R 4 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7741 (t) REVERT: R 32 TYR cc_start: 0.7725 (m-80) cc_final: 0.7265 (m-80) REVERT: R 100 GLN cc_start: 0.7690 (mp10) cc_final: 0.7328 (mp10) REVERT: S 2 VAL cc_start: 0.8207 (t) cc_final: 0.8005 (p) REVERT: S 78 ASN cc_start: 0.6253 (t0) cc_final: 0.5969 (t0) REVERT: T 100 GLN cc_start: 0.7960 (mp10) cc_final: 0.7601 (mp10) outliers start: 74 outliers final: 57 residues processed: 517 average time/residue: 0.1577 time to fit residues: 126.4969 Evaluate side-chains 538 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 474 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 227 ASN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain J residue 113 GLN Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 125 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN C 27 ASN ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN F 437 ASN T 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.150351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128545 restraints weight = 31360.726| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.25 r_work: 0.3519 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21459 Z= 0.159 Angle : 0.567 14.276 29181 Z= 0.291 Chirality : 0.044 0.210 3357 Planarity : 0.004 0.056 3699 Dihedral : 4.543 32.587 2934 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.42 % Allowed : 16.90 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2682 helix: 1.00 (0.26), residues: 396 sheet: 0.34 (0.17), residues: 888 loop : -0.31 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 336 TYR 0.019 0.002 TYR B 306 PHE 0.026 0.002 PHE F 223 TRP 0.022 0.002 TRP T 35 HIS 0.004 0.001 HIS S 99 Details of bonding type rmsd covalent geometry : bond 0.00353 (21426) covalent geometry : angle 0.56637 (29115) SS BOND : bond 0.00292 ( 33) SS BOND : angle 0.85071 ( 66) hydrogen bonds : bond 0.03280 ( 901) hydrogen bonds : angle 5.42849 ( 2427) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 483 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 CYS cc_start: 0.7311 (t) cc_final: 0.7011 (t) REVERT: A 87 LYS cc_start: 0.8362 (mmtt) cc_final: 0.8027 (mmtp) REVERT: B 190 SER cc_start: 0.8545 (t) cc_final: 0.8231 (m) REVERT: B 227 ASN cc_start: 0.7811 (t0) cc_final: 0.7451 (m110) REVERT: B 228 ASN cc_start: 0.8043 (t0) cc_final: 0.7474 (t0) REVERT: B 256 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7277 (mt-10) REVERT: B 259 SER cc_start: 0.8194 (t) cc_final: 0.7459 (p) REVERT: B 263 ASP cc_start: 0.7748 (m-30) cc_final: 0.7212 (m-30) REVERT: B 284 GLN cc_start: 0.7816 (mt0) cc_final: 0.7527 (mt0) REVERT: B 338 ASP cc_start: 0.8030 (p0) cc_final: 0.7563 (p0) REVERT: B 393 CYS cc_start: 0.6442 (m) cc_final: 0.6121 (m) REVERT: B 465 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7911 (ttpt) REVERT: C 44 TYR cc_start: 0.8725 (m-80) cc_final: 0.8103 (m-80) REVERT: D 190 SER cc_start: 0.8648 (t) cc_final: 0.8139 (p) REVERT: D 224 GLN cc_start: 0.8255 (mt0) cc_final: 0.8016 (mt0) REVERT: D 240 ASN cc_start: 0.8110 (m-40) cc_final: 0.7840 (m-40) REVERT: D 270 GLN cc_start: 0.7988 (mt0) cc_final: 0.7557 (mt0) REVERT: D 319 SER cc_start: 0.8527 (t) cc_final: 0.8059 (p) REVERT: D 399 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8310 (mttm) REVERT: D 441 TYR cc_start: 0.8668 (t80) cc_final: 0.8345 (t80) REVERT: D 487 GLU cc_start: 0.6503 (mp0) cc_final: 0.5441 (mp0) REVERT: F 190 SER cc_start: 0.8806 (t) cc_final: 0.8405 (p) REVERT: F 227 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7909 (t0) REVERT: F 263 ASP cc_start: 0.7452 (m-30) cc_final: 0.7130 (m-30) REVERT: F 284 GLN cc_start: 0.8005 (mt0) cc_final: 0.7743 (mt0) REVERT: F 286 TYR cc_start: 0.8481 (m-80) cc_final: 0.7828 (m-80) REVERT: F 338 ASP cc_start: 0.7905 (p0) cc_final: 0.7463 (p0) REVERT: F 361 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7599 (mm-40) REVERT: F 371 ASN cc_start: 0.8141 (p0) cc_final: 0.7931 (p0) REVERT: F 399 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8434 (mttp) REVERT: H 28 SER cc_start: 0.8567 (p) cc_final: 0.8252 (p) REVERT: H 80 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: H 98 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7793 (mtp180) REVERT: H 99 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: I 23 LYS cc_start: 0.7966 (tttm) cc_final: 0.7730 (ttpp) REVERT: I 70 MET cc_start: 0.7377 (mpp) cc_final: 0.6745 (mpp) REVERT: I 77 ASN cc_start: 0.8671 (t0) cc_final: 0.8236 (t0) REVERT: I 81 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6473 (tmm) REVERT: I 110 TYR cc_start: 0.7956 (m-10) cc_final: 0.7591 (m-10) REVERT: J 47 TRP cc_start: 0.8467 (t60) cc_final: 0.7761 (t60) REVERT: J 70 MET cc_start: 0.7343 (mpp) cc_final: 0.7004 (mpp) REVERT: L 22 SER cc_start: 0.7266 (p) cc_final: 0.6973 (p) REVERT: L 94 MET cc_start: 0.7882 (tmm) cc_final: 0.7537 (tmm) REVERT: N 22 SER cc_start: 0.7703 (p) cc_final: 0.7439 (p) REVERT: N 63 VAL cc_start: 0.7678 (t) cc_final: 0.7428 (p) REVERT: N 66 ARG cc_start: 0.7080 (ttm170) cc_final: 0.6631 (ttm170) REVERT: N 103 PHE cc_start: 0.8327 (m-80) cc_final: 0.8090 (m-80) REVERT: O 87 MET cc_start: 0.6859 (mmm) cc_final: 0.4707 (ptp) REVERT: P 4 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7724 (t) REVERT: R 4 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7752 (t) REVERT: R 32 TYR cc_start: 0.7670 (m-80) cc_final: 0.7242 (m-80) REVERT: R 48 ILE cc_start: 0.7858 (mm) cc_final: 0.7589 (mm) REVERT: R 100 GLN cc_start: 0.7687 (mp10) cc_final: 0.7320 (mp10) REVERT: S 78 ASN cc_start: 0.6233 (t0) cc_final: 0.5939 (t0) REVERT: T 100 GLN cc_start: 0.7937 (mp10) cc_final: 0.7556 (mp10) outliers start: 82 outliers final: 63 residues processed: 521 average time/residue: 0.1470 time to fit residues: 118.9821 Evaluate side-chains 550 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 480 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 227 ASN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain J residue 113 GLN Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 181 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 250 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 37 optimal weight: 0.0010 chunk 103 optimal weight: 0.6980 chunk 196 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN B 494 GLN C 27 ASN D 363 ASN ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN F 437 ASN O 79 GLN T 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.151132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129414 restraints weight = 31158.474| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.25 r_work: 0.3554 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21459 Z= 0.141 Angle : 0.562 14.045 29181 Z= 0.287 Chirality : 0.044 0.241 3357 Planarity : 0.004 0.056 3699 Dihedral : 4.486 31.932 2934 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.34 % Allowed : 17.56 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2682 helix: 1.04 (0.26), residues: 396 sheet: 0.39 (0.17), residues: 888 loop : -0.28 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.017 0.002 TYR F 306 PHE 0.019 0.001 PHE D 223 TRP 0.023 0.002 TRP T 35 HIS 0.004 0.001 HIS S 99 Details of bonding type rmsd covalent geometry : bond 0.00313 (21426) covalent geometry : angle 0.56149 (29115) SS BOND : bond 0.00261 ( 33) SS BOND : angle 0.86058 ( 66) hydrogen bonds : bond 0.03138 ( 901) hydrogen bonds : angle 5.35199 ( 2427) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 476 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 CYS cc_start: 0.7298 (t) cc_final: 0.6985 (t) REVERT: B 190 SER cc_start: 0.8557 (t) cc_final: 0.8247 (m) REVERT: B 227 ASN cc_start: 0.7910 (t0) cc_final: 0.7565 (m110) REVERT: B 228 ASN cc_start: 0.8032 (t0) cc_final: 0.7452 (t0) REVERT: B 256 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7221 (mt-10) REVERT: B 259 SER cc_start: 0.8157 (t) cc_final: 0.7696 (p) REVERT: B 263 ASP cc_start: 0.7703 (m-30) cc_final: 0.7148 (m-30) REVERT: B 284 GLN cc_start: 0.7762 (mt0) cc_final: 0.7466 (mt0) REVERT: B 338 ASP cc_start: 0.7998 (p0) cc_final: 0.7533 (p0) REVERT: B 393 CYS cc_start: 0.6429 (m) cc_final: 0.6137 (m) REVERT: B 465 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7889 (ttpt) REVERT: C 44 TYR cc_start: 0.8725 (m-80) cc_final: 0.8056 (m-80) REVERT: D 190 SER cc_start: 0.8648 (t) cc_final: 0.8132 (p) REVERT: D 224 GLN cc_start: 0.8235 (mt0) cc_final: 0.7995 (mt0) REVERT: D 227 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7580 (t0) REVERT: D 240 ASN cc_start: 0.8104 (m-40) cc_final: 0.7835 (m-40) REVERT: D 270 GLN cc_start: 0.7975 (mt0) cc_final: 0.7545 (mt0) REVERT: D 319 SER cc_start: 0.8529 (t) cc_final: 0.8129 (p) REVERT: D 399 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8294 (mttm) REVERT: D 487 GLU cc_start: 0.6509 (mp0) cc_final: 0.5637 (mp0) REVERT: F 227 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7881 (t0) REVERT: F 228 ASN cc_start: 0.8204 (t0) cc_final: 0.7940 (t0) REVERT: F 263 ASP cc_start: 0.7406 (m-30) cc_final: 0.7099 (m-30) REVERT: F 284 GLN cc_start: 0.8001 (mt0) cc_final: 0.7734 (mt0) REVERT: F 286 TYR cc_start: 0.8433 (m-80) cc_final: 0.7810 (m-80) REVERT: F 338 ASP cc_start: 0.7877 (p0) cc_final: 0.7441 (p0) REVERT: F 361 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7618 (mm-40) REVERT: F 399 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8475 (mttm) REVERT: F 451 SER cc_start: 0.8384 (t) cc_final: 0.7926 (m) REVERT: H 28 SER cc_start: 0.8558 (p) cc_final: 0.8188 (p) REVERT: H 77 ASN cc_start: 0.8437 (t0) cc_final: 0.8108 (t0) REVERT: H 80 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.4973 (m-80) REVERT: H 98 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7785 (mtp180) REVERT: H 99 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: H 110 TYR cc_start: 0.8380 (m-80) cc_final: 0.8111 (m-10) REVERT: I 23 LYS cc_start: 0.7949 (tttm) cc_final: 0.7711 (ttpp) REVERT: I 70 MET cc_start: 0.7361 (mpp) cc_final: 0.6739 (mpp) REVERT: I 77 ASN cc_start: 0.8673 (t0) cc_final: 0.8261 (t0) REVERT: I 81 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6471 (tmm) REVERT: I 110 TYR cc_start: 0.7910 (m-10) cc_final: 0.7654 (m-80) REVERT: J 28 SER cc_start: 0.8531 (p) cc_final: 0.8318 (p) REVERT: J 47 TRP cc_start: 0.8486 (t60) cc_final: 0.7800 (t60) REVERT: J 70 MET cc_start: 0.7337 (mpp) cc_final: 0.6974 (mpp) REVERT: J 81 MET cc_start: 0.6599 (tmm) cc_final: 0.6361 (tmm) REVERT: L 22 SER cc_start: 0.7259 (p) cc_final: 0.6983 (p) REVERT: L 94 MET cc_start: 0.7869 (tmm) cc_final: 0.7559 (tmm) REVERT: N 22 SER cc_start: 0.7694 (p) cc_final: 0.7441 (p) REVERT: N 63 VAL cc_start: 0.7690 (t) cc_final: 0.7445 (p) REVERT: N 66 ARG cc_start: 0.7082 (ttm170) cc_final: 0.6631 (ttm170) REVERT: N 103 PHE cc_start: 0.8345 (m-80) cc_final: 0.8096 (m-80) REVERT: O 87 MET cc_start: 0.6776 (mmm) cc_final: 0.5000 (ptp) REVERT: P 4 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7726 (t) REVERT: Q 78 ASN cc_start: 0.7108 (t0) cc_final: 0.6772 (t0) REVERT: R 4 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7757 (t) REVERT: R 32 TYR cc_start: 0.7608 (m-80) cc_final: 0.7256 (m-80) REVERT: R 48 ILE cc_start: 0.7819 (mm) cc_final: 0.7555 (mm) REVERT: R 100 GLN cc_start: 0.7697 (mp10) cc_final: 0.7324 (mp10) REVERT: S 78 ASN cc_start: 0.6245 (t0) cc_final: 0.5952 (t0) REVERT: T 4 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7518 (t) REVERT: T 100 GLN cc_start: 0.7918 (mp10) cc_final: 0.7548 (mp10) outliers start: 80 outliers final: 64 residues processed: 513 average time/residue: 0.1472 time to fit residues: 117.3563 Evaluate side-chains 543 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 470 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 227 ASN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 195 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN B 462 GLN B 494 GLN C 27 ASN ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN F 437 ASN S 79 GLN ** T 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.150054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127642 restraints weight = 31199.923| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.40 r_work: 0.3502 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21459 Z= 0.184 Angle : 0.586 13.697 29181 Z= 0.302 Chirality : 0.045 0.208 3357 Planarity : 0.004 0.056 3699 Dihedral : 4.623 33.786 2934 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.50 % Allowed : 17.81 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2682 helix: 0.83 (0.26), residues: 396 sheet: 0.35 (0.17), residues: 888 loop : -0.31 (0.18), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 336 TYR 0.023 0.002 TYR N 54 PHE 0.030 0.002 PHE F 223 TRP 0.026 0.002 TRP T 35 HIS 0.005 0.002 HIS S 99 Details of bonding type rmsd covalent geometry : bond 0.00411 (21426) covalent geometry : angle 0.58450 (29115) SS BOND : bond 0.00282 ( 33) SS BOND : angle 0.93000 ( 66) hydrogen bonds : bond 0.03398 ( 901) hydrogen bonds : angle 5.41720 ( 2427) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 482 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 CYS cc_start: 0.7387 (t) cc_final: 0.7104 (t) REVERT: B 190 SER cc_start: 0.8568 (t) cc_final: 0.8238 (m) REVERT: B 227 ASN cc_start: 0.7947 (t0) cc_final: 0.7601 (m110) REVERT: B 228 ASN cc_start: 0.8062 (t0) cc_final: 0.7511 (t0) REVERT: B 256 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7289 (mt-10) REVERT: B 259 SER cc_start: 0.8156 (t) cc_final: 0.7846 (p) REVERT: B 338 ASP cc_start: 0.8023 (p0) cc_final: 0.7567 (p0) REVERT: B 465 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7921 (ttpt) REVERT: C 44 TYR cc_start: 0.8735 (m-80) cc_final: 0.8067 (m-80) REVERT: D 190 SER cc_start: 0.8658 (t) cc_final: 0.8157 (p) REVERT: D 224 GLN cc_start: 0.8312 (mt0) cc_final: 0.8079 (mt0) REVERT: D 227 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7563 (t0) REVERT: D 232 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: D 240 ASN cc_start: 0.8140 (m-40) cc_final: 0.7877 (m-40) REVERT: D 270 GLN cc_start: 0.7961 (mt0) cc_final: 0.7548 (mt0) REVERT: D 319 SER cc_start: 0.8590 (t) cc_final: 0.8123 (p) REVERT: D 399 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8325 (mttm) REVERT: D 441 TYR cc_start: 0.8673 (t80) cc_final: 0.8388 (t80) REVERT: D 487 GLU cc_start: 0.6530 (mp0) cc_final: 0.5696 (mp0) REVERT: F 227 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7894 (t0) REVERT: F 263 ASP cc_start: 0.7463 (m-30) cc_final: 0.7192 (m-30) REVERT: F 274 MET cc_start: 0.8101 (mtt) cc_final: 0.7749 (mtt) REVERT: F 284 GLN cc_start: 0.8077 (mt0) cc_final: 0.7702 (mt0) REVERT: F 338 ASP cc_start: 0.7925 (p0) cc_final: 0.7482 (p0) REVERT: F 361 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7631 (mm-40) REVERT: F 392 ASP cc_start: 0.7025 (p0) cc_final: 0.6731 (p0) REVERT: F 399 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8490 (mttp) REVERT: F 426 ASN cc_start: 0.8012 (t0) cc_final: 0.7629 (t0) REVERT: F 441 TYR cc_start: 0.8705 (t80) cc_final: 0.8274 (t80) REVERT: F 451 SER cc_start: 0.8332 (t) cc_final: 0.7883 (m) REVERT: H 28 SER cc_start: 0.8568 (p) cc_final: 0.8239 (p) REVERT: H 77 ASN cc_start: 0.8502 (t0) cc_final: 0.8164 (t0) REVERT: H 80 TYR cc_start: 0.6357 (OUTLIER) cc_final: 0.4992 (m-80) REVERT: H 98 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7864 (mtp180) REVERT: H 99 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: I 70 MET cc_start: 0.7389 (mpp) cc_final: 0.6783 (mpp) REVERT: I 73 ASP cc_start: 0.7712 (t70) cc_final: 0.6906 (t70) REVERT: I 77 ASN cc_start: 0.8691 (t0) cc_final: 0.8261 (t0) REVERT: I 81 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6490 (tmm) REVERT: I 110 TYR cc_start: 0.7940 (m-10) cc_final: 0.7722 (m-10) REVERT: J 28 SER cc_start: 0.8541 (p) cc_final: 0.8333 (p) REVERT: J 47 TRP cc_start: 0.8492 (t60) cc_final: 0.8147 (t60) REVERT: J 70 MET cc_start: 0.7391 (mpp) cc_final: 0.7020 (mpp) REVERT: J 81 MET cc_start: 0.6761 (tmm) cc_final: 0.6481 (tmm) REVERT: L 22 SER cc_start: 0.7312 (p) cc_final: 0.7036 (p) REVERT: L 84 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7495 (mt-10) REVERT: M 31 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7074 (t80) REVERT: M 63 VAL cc_start: 0.7519 (t) cc_final: 0.7286 (p) REVERT: N 22 SER cc_start: 0.7725 (p) cc_final: 0.7471 (p) REVERT: N 63 VAL cc_start: 0.7745 (t) cc_final: 0.7491 (p) REVERT: N 66 ARG cc_start: 0.7076 (ttm170) cc_final: 0.6607 (ttm170) REVERT: N 103 PHE cc_start: 0.8374 (m-80) cc_final: 0.8120 (m-80) REVERT: P 4 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7738 (t) REVERT: P 55 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6397 (tp-100) REVERT: Q 78 ASN cc_start: 0.7088 (t0) cc_final: 0.6760 (t0) REVERT: R 4 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7749 (t) REVERT: R 32 TYR cc_start: 0.7605 (m-80) cc_final: 0.7301 (m-80) REVERT: R 48 ILE cc_start: 0.7875 (mm) cc_final: 0.7620 (mm) REVERT: R 100 GLN cc_start: 0.7733 (mp10) cc_final: 0.7365 (mp10) REVERT: T 4 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7469 (t) REVERT: T 100 GLN cc_start: 0.7991 (mp10) cc_final: 0.7600 (mp10) outliers start: 84 outliers final: 67 residues processed: 522 average time/residue: 0.1503 time to fit residues: 122.0985 Evaluate side-chains 558 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 479 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 227 ASN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 55 GLN Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 57 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN C 27 ASN D 363 ASN ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN F 437 ASN M 43 GLN ** T 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128924 restraints weight = 31433.076| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.25 r_work: 0.3535 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21459 Z= 0.181 Angle : 0.598 20.467 29181 Z= 0.304 Chirality : 0.045 0.199 3357 Planarity : 0.004 0.056 3699 Dihedral : 4.639 35.024 2934 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.59 % Allowed : 17.94 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2682 helix: 0.84 (0.26), residues: 393 sheet: 0.35 (0.17), residues: 888 loop : -0.32 (0.18), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 336 TYR 0.024 0.002 TYR B 306 PHE 0.031 0.002 PHE F 223 TRP 0.022 0.002 TRP T 35 HIS 0.005 0.002 HIS S 99 Details of bonding type rmsd covalent geometry : bond 0.00404 (21426) covalent geometry : angle 0.59692 (29115) SS BOND : bond 0.00284 ( 33) SS BOND : angle 0.90651 ( 66) hydrogen bonds : bond 0.03378 ( 901) hydrogen bonds : angle 5.40015 ( 2427) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 480 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 CYS cc_start: 0.7326 (t) cc_final: 0.7043 (t) REVERT: A 87 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8061 (mmtp) REVERT: B 190 SER cc_start: 0.8536 (t) cc_final: 0.8233 (m) REVERT: B 227 ASN cc_start: 0.7884 (t0) cc_final: 0.7624 (m110) REVERT: B 228 ASN cc_start: 0.8033 (t0) cc_final: 0.7478 (t0) REVERT: B 256 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7233 (mt-10) REVERT: B 259 SER cc_start: 0.8194 (t) cc_final: 0.7513 (p) REVERT: B 263 ASP cc_start: 0.7816 (m-30) cc_final: 0.7173 (m-30) REVERT: B 284 GLN cc_start: 0.7779 (mt0) cc_final: 0.7534 (mt0) REVERT: B 338 ASP cc_start: 0.7941 (p0) cc_final: 0.7491 (p0) REVERT: B 465 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7866 (ttpt) REVERT: C 44 TYR cc_start: 0.8753 (m-80) cc_final: 0.8103 (m-80) REVERT: D 224 GLN cc_start: 0.8218 (mt0) cc_final: 0.7976 (mt0) REVERT: D 227 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7584 (t0) REVERT: D 232 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: D 240 ASN cc_start: 0.8133 (m-40) cc_final: 0.7870 (m-40) REVERT: D 251 MET cc_start: 0.8228 (mmm) cc_final: 0.8020 (mmp) REVERT: D 270 GLN cc_start: 0.7984 (mt0) cc_final: 0.7514 (mt0) REVERT: D 319 SER cc_start: 0.8571 (t) cc_final: 0.8128 (p) REVERT: D 399 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8305 (mttm) REVERT: D 441 TYR cc_start: 0.8657 (t80) cc_final: 0.8365 (t80) REVERT: D 487 GLU cc_start: 0.6562 (mp0) cc_final: 0.5769 (mp0) REVERT: F 227 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7854 (t0) REVERT: F 263 ASP cc_start: 0.7407 (m-30) cc_final: 0.7119 (m-30) REVERT: F 274 MET cc_start: 0.8074 (mtt) cc_final: 0.7776 (mtt) REVERT: F 284 GLN cc_start: 0.8005 (mt0) cc_final: 0.7758 (mt0) REVERT: F 338 ASP cc_start: 0.7805 (p0) cc_final: 0.7367 (p0) REVERT: F 361 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7630 (mm-40) REVERT: F 392 ASP cc_start: 0.7048 (p0) cc_final: 0.6758 (p0) REVERT: F 399 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8469 (mttp) REVERT: F 426 ASN cc_start: 0.8014 (t0) cc_final: 0.7626 (t0) REVERT: F 441 TYR cc_start: 0.8673 (t80) cc_final: 0.8277 (t80) REVERT: H 28 SER cc_start: 0.8556 (p) cc_final: 0.8244 (p) REVERT: H 77 ASN cc_start: 0.8548 (t0) cc_final: 0.8223 (t0) REVERT: H 80 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5016 (m-80) REVERT: H 98 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7873 (mtp180) REVERT: H 99 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: H 110 TYR cc_start: 0.8370 (m-80) cc_final: 0.8100 (m-10) REVERT: I 70 MET cc_start: 0.7329 (mpp) cc_final: 0.6760 (mpp) REVERT: I 73 ASP cc_start: 0.7692 (t70) cc_final: 0.6916 (t70) REVERT: I 77 ASN cc_start: 0.8704 (t0) cc_final: 0.8279 (t0) REVERT: I 81 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6502 (tmm) REVERT: I 110 TYR cc_start: 0.7891 (m-10) cc_final: 0.7682 (m-10) REVERT: J 28 SER cc_start: 0.8579 (p) cc_final: 0.8365 (p) REVERT: J 47 TRP cc_start: 0.8454 (t60) cc_final: 0.8113 (t60) REVERT: J 70 MET cc_start: 0.7326 (mpp) cc_final: 0.7034 (mpp) REVERT: J 81 MET cc_start: 0.6708 (tmm) cc_final: 0.6436 (tmm) REVERT: L 22 SER cc_start: 0.7308 (p) cc_final: 0.7011 (p) REVERT: L 84 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7386 (mt-10) REVERT: M 31 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7025 (t80) REVERT: M 63 VAL cc_start: 0.7546 (t) cc_final: 0.7323 (p) REVERT: N 22 SER cc_start: 0.7713 (p) cc_final: 0.7459 (p) REVERT: N 63 VAL cc_start: 0.7752 (t) cc_final: 0.7514 (p) REVERT: N 66 ARG cc_start: 0.7118 (ttm170) cc_final: 0.6678 (ttm170) REVERT: O 87 MET cc_start: 0.6889 (mmm) cc_final: 0.3980 (ptm) REVERT: P 4 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7751 (t) REVERT: P 55 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6427 (tp-100) REVERT: Q 78 ASN cc_start: 0.7088 (t0) cc_final: 0.6743 (t0) REVERT: R 4 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7791 (t) REVERT: R 32 TYR cc_start: 0.7540 (m-80) cc_final: 0.7313 (m-80) REVERT: R 48 ILE cc_start: 0.7899 (mm) cc_final: 0.7652 (mm) REVERT: R 100 GLN cc_start: 0.7690 (mp10) cc_final: 0.7346 (mp10) REVERT: T 4 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7501 (t) REVERT: T 100 GLN cc_start: 0.7925 (mp10) cc_final: 0.7569 (mp10) outliers start: 86 outliers final: 74 residues processed: 519 average time/residue: 0.1496 time to fit residues: 121.1442 Evaluate side-chains 564 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 478 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 227 ASN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain J residue 113 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 55 GLN Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 262 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 235 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 47 optimal weight: 0.0270 chunk 255 optimal weight: 0.6980 chunk 176 optimal weight: 0.0270 chunk 127 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 363 ASN C 27 ASN ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN F 437 ASN ** T 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.151834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130109 restraints weight = 31200.613| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.24 r_work: 0.3545 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21459 Z= 0.125 Angle : 0.570 18.441 29181 Z= 0.289 Chirality : 0.044 0.220 3357 Planarity : 0.004 0.119 3699 Dihedral : 4.447 33.787 2934 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.05 % Allowed : 18.73 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2682 helix: 0.96 (0.26), residues: 396 sheet: 0.43 (0.17), residues: 897 loop : -0.26 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 66 TYR 0.022 0.002 TYR B 306 PHE 0.019 0.001 PHE D 223 TRP 0.019 0.001 TRP T 35 HIS 0.004 0.001 HIS Q 99 Details of bonding type rmsd covalent geometry : bond 0.00276 (21426) covalent geometry : angle 0.56897 (29115) SS BOND : bond 0.00248 ( 33) SS BOND : angle 0.83002 ( 66) hydrogen bonds : bond 0.03074 ( 901) hydrogen bonds : angle 5.23507 ( 2427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5813.32 seconds wall clock time: 100 minutes 22.02 seconds (6022.02 seconds total)