Starting phenix.real_space_refine on Tue Aug 26 09:20:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iqo_60792/08_2025/9iqo_60792.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iqo_60792/08_2025/9iqo_60792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iqo_60792/08_2025/9iqo_60792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iqo_60792/08_2025/9iqo_60792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iqo_60792/08_2025/9iqo_60792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iqo_60792/08_2025/9iqo_60792.map" } resolution = 1.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 200 5.16 5 C 22984 2.51 5 N 6296 2.21 5 O 6616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36096 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 433} Chain: "a" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 933 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "C" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 433} Chain: "D" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 433} Chain: "B" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 433} Chain: "H" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 433} Chain: "E" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 433} Chain: "F" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 433} Chain: "G" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 433} Chain: "c" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 933 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "d" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 933 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "b" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 933 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "h" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 933 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "e" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 933 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 933 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "g" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 933 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Time building chain proxies: 6.25, per 1000 atoms: 0.17 Number of scatterers: 36096 At special positions: 0 Unit cell: (139.08, 139.08, 120.84, 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 200 16.00 O 6616 8.00 N 6296 7.00 C 22984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.84 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 32 sheets defined 50.1% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 145 through 155 removed outlier: 4.288A pdb=" N VAL A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.510A pdb=" N GLY A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 225 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.691A pdb=" N LEU A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 387 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 404 through 425 Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.949A pdb=" N VAL A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'a' and resid 13 through 17 Processing helix chain 'a' and resid 29 through 43 Processing helix chain 'a' and resid 53 through 57 Processing helix chain 'a' and resid 74 through 89 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 41 through 54 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 115 through 119 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 145 through 155 removed outlier: 4.264A pdb=" N VAL C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 188 removed outlier: 3.577A pdb=" N GLY C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 225 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 265 through 280 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.616A pdb=" N LEU C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 Processing helix chain 'C' and resid 327 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 378 through 387 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 404 through 425 Processing helix chain 'C' and resid 432 through 442 removed outlier: 3.803A pdb=" N VAL C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 454 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 41 through 54 Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 133 through 138 Processing helix chain 'D' and resid 145 through 155 removed outlier: 4.288A pdb=" N VAL D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 188 removed outlier: 3.515A pdb=" N GLY D 188 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 225 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 265 through 280 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.706A pdb=" N LEU D 293 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 Processing helix chain 'D' and resid 327 through 343 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 425 Processing helix chain 'D' and resid 432 through 442 removed outlier: 3.862A pdb=" N VAL D 436 " --> pdb=" O GLU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 454 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 41 through 54 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 115 through 119 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 145 through 155 removed outlier: 4.288A pdb=" N VAL B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.544A pdb=" N GLY B 188 " --> pdb=" O CYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'B' and resid 265 through 280 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.672A pdb=" N LEU B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 327 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 378 through 387 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 425 Processing helix chain 'B' and resid 432 through 442 removed outlier: 3.884A pdb=" N VAL B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 454 Processing helix chain 'H' and resid 12 through 17 Processing helix chain 'H' and resid 41 through 54 Processing helix chain 'H' and resid 61 through 67 Processing helix chain 'H' and resid 68 through 73 Processing helix chain 'H' and resid 96 through 100 Processing helix chain 'H' and resid 104 through 114 Processing helix chain 'H' and resid 115 through 119 Processing helix chain 'H' and resid 133 through 138 Processing helix chain 'H' and resid 145 through 155 removed outlier: 4.287A pdb=" N VAL H 149 " --> pdb=" O HIS H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 188 removed outlier: 3.513A pdb=" N GLY H 188 " --> pdb=" O CYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 225 Processing helix chain 'H' and resid 238 through 252 Processing helix chain 'H' and resid 265 through 280 Processing helix chain 'H' and resid 289 through 295 removed outlier: 3.691A pdb=" N LEU H 293 " --> pdb=" O MET H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 314 Processing helix chain 'H' and resid 327 through 343 Processing helix chain 'H' and resid 349 through 353 Processing helix chain 'H' and resid 375 through 377 No H-bonds generated for 'chain 'H' and resid 375 through 377' Processing helix chain 'H' and resid 378 through 387 Processing helix chain 'H' and resid 395 through 400 Processing helix chain 'H' and resid 404 through 425 Processing helix chain 'H' and resid 432 through 442 removed outlier: 3.871A pdb=" N VAL H 436 " --> pdb=" O GLU H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 454 Processing helix chain 'E' and resid 12 through 17 Processing helix chain 'E' and resid 41 through 54 Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 96 through 100 Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 115 through 119 Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 145 through 155 removed outlier: 4.262A pdb=" N VAL E 149 " --> pdb=" O HIS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 188 removed outlier: 3.547A pdb=" N GLY E 188 " --> pdb=" O CYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 225 Processing helix chain 'E' and resid 238 through 252 Processing helix chain 'E' and resid 265 through 280 Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.657A pdb=" N LEU E 293 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'E' and resid 327 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 375 through 377 No H-bonds generated for 'chain 'E' and resid 375 through 377' Processing helix chain 'E' and resid 378 through 387 Processing helix chain 'E' and resid 395 through 400 Processing helix chain 'E' and resid 404 through 425 Processing helix chain 'E' and resid 432 through 442 removed outlier: 3.771A pdb=" N VAL E 436 " --> pdb=" O GLU E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 454 Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 41 through 54 Processing helix chain 'F' and resid 61 through 67 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 96 through 100 Processing helix chain 'F' and resid 104 through 114 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 145 through 155 removed outlier: 4.288A pdb=" N VAL F 149 " --> pdb=" O HIS F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 188 removed outlier: 3.544A pdb=" N GLY F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 225 Processing helix chain 'F' and resid 238 through 252 Processing helix chain 'F' and resid 265 through 280 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.693A pdb=" N LEU F 293 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 314 Processing helix chain 'F' and resid 327 through 343 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 378 through 387 Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 404 through 425 Processing helix chain 'F' and resid 432 through 442 removed outlier: 3.879A pdb=" N VAL F 436 " --> pdb=" O GLU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 454 Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 41 through 54 Processing helix chain 'G' and resid 61 through 67 Processing helix chain 'G' and resid 68 through 73 Processing helix chain 'G' and resid 96 through 100 Processing helix chain 'G' and resid 104 through 114 Processing helix chain 'G' and resid 115 through 119 Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 145 through 155 removed outlier: 4.263A pdb=" N VAL G 149 " --> pdb=" O HIS G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 188 removed outlier: 3.548A pdb=" N GLY G 188 " --> pdb=" O CYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 Processing helix chain 'G' and resid 238 through 252 Processing helix chain 'G' and resid 265 through 280 Processing helix chain 'G' and resid 289 through 295 removed outlier: 3.618A pdb=" N LEU G 293 " --> pdb=" O MET G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 314 Processing helix chain 'G' and resid 327 through 343 Processing helix chain 'G' and resid 349 through 353 Processing helix chain 'G' and resid 375 through 377 No H-bonds generated for 'chain 'G' and resid 375 through 377' Processing helix chain 'G' and resid 378 through 387 Processing helix chain 'G' and resid 395 through 400 Processing helix chain 'G' and resid 404 through 425 Processing helix chain 'G' and resid 432 through 442 removed outlier: 3.793A pdb=" N VAL G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 454 Processing helix chain 'c' and resid 13 through 17 Processing helix chain 'c' and resid 29 through 43 Processing helix chain 'c' and resid 53 through 57 Processing helix chain 'c' and resid 74 through 89 Processing helix chain 'd' and resid 13 through 17 Processing helix chain 'd' and resid 29 through 43 Processing helix chain 'd' and resid 53 through 57 Processing helix chain 'd' and resid 74 through 89 Processing helix chain 'b' and resid 13 through 17 Processing helix chain 'b' and resid 29 through 43 Processing helix chain 'b' and resid 53 through 57 Processing helix chain 'b' and resid 74 through 89 Processing helix chain 'h' and resid 13 through 17 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 53 through 57 Processing helix chain 'h' and resid 74 through 89 Processing helix chain 'e' and resid 13 through 17 Processing helix chain 'e' and resid 29 through 43 Processing helix chain 'e' and resid 53 through 57 Processing helix chain 'e' and resid 74 through 89 Processing helix chain 'f' and resid 13 through 17 Processing helix chain 'f' and resid 29 through 43 Processing helix chain 'f' and resid 53 through 57 Processing helix chain 'f' and resid 74 through 89 Processing helix chain 'g' and resid 13 through 17 Processing helix chain 'g' and resid 29 through 43 Processing helix chain 'g' and resid 53 through 57 Processing helix chain 'g' and resid 74 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 81 removed outlier: 6.720A pdb=" N PHE A 92 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE A 79 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR A 90 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 129 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS A 33 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU A 127 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR A 35 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU A 125 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 163 removed outlier: 6.516A pdb=" N LEU A 161 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA A 368 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN A 393 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA A 370 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 318 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 257 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS A 286 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N HIS A 259 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS A 230 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET A 258 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU A 232 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASP A 260 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR A 192 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN A 233 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'a' and resid 63 through 64 removed outlier: 6.599A pdb=" N VAL a 94 " --> pdb=" O ILE a 112 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP a 100 " --> pdb=" O LYS a 106 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYS a 106 " --> pdb=" O ASP a 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 75 through 81 removed outlier: 5.580A pdb=" N ALA C 76 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 94 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 78 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS C 33 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU C 127 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 35 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU C 125 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N GLY C 300 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU C 125 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.492A pdb=" N LEU C 161 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA C 368 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN C 393 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 370 " --> pdb=" O GLN C 393 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 318 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE C 257 " --> pdb=" O HIS C 284 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N HIS C 286 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS C 259 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HIS C 230 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET C 258 " --> pdb=" O HIS C 230 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU C 232 " --> pdb=" O MET C 258 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ASP C 260 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR C 192 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ASN C 233 " --> pdb=" O THR C 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AA8, first strand: chain 'D' and resid 75 through 81 removed outlier: 6.721A pdb=" N PHE D 92 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE D 79 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR D 90 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP D 129 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS D 33 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU D 127 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR D 35 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU D 125 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 161 through 163 removed outlier: 6.515A pdb=" N LEU D 161 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA D 368 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN D 393 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA D 370 " --> pdb=" O GLN D 393 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 318 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 257 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS D 286 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N HIS D 259 " --> pdb=" O HIS D 286 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N HIS D 230 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET D 258 " --> pdb=" O HIS D 230 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU D 232 " --> pdb=" O MET D 258 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASP D 260 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR D 192 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN D 233 " --> pdb=" O THR D 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 345 through 346 Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 81 removed outlier: 6.721A pdb=" N PHE B 92 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE B 79 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR B 90 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP B 129 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS B 33 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU B 127 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 35 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU B 125 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N GLY B 300 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 125 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 161 through 163 removed outlier: 6.527A pdb=" N LEU B 161 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 368 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLN B 393 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 370 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 318 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE B 257 " --> pdb=" O HIS B 284 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N HIS B 286 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS B 259 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N HIS B 230 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET B 258 " --> pdb=" O HIS B 230 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU B 232 " --> pdb=" O MET B 258 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ASP B 260 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR B 192 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN B 233 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 345 through 346 Processing sheet with id=AB5, first strand: chain 'H' and resid 75 through 81 removed outlier: 6.720A pdb=" N PHE H 92 " --> pdb=" O TYR H 77 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE H 79 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR H 90 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP H 129 " --> pdb=" O CYS H 31 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS H 33 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU H 127 " --> pdb=" O LYS H 33 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR H 35 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU H 125 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N GLY H 300 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU H 125 " --> pdb=" O GLY H 300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 161 through 163 removed outlier: 6.508A pdb=" N LEU H 161 " --> pdb=" O LEU H 392 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA H 368 " --> pdb=" O VAL H 391 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN H 393 " --> pdb=" O ALA H 368 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA H 370 " --> pdb=" O GLN H 393 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU H 318 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE H 257 " --> pdb=" O HIS H 284 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS H 286 " --> pdb=" O ILE H 257 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS H 259 " --> pdb=" O HIS H 286 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N HIS H 230 " --> pdb=" O ILE H 256 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET H 258 " --> pdb=" O HIS H 230 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU H 232 " --> pdb=" O MET H 258 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASP H 260 " --> pdb=" O LEU H 232 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR H 192 " --> pdb=" O TYR H 231 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN H 233 " --> pdb=" O THR H 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 345 through 346 Processing sheet with id=AB8, first strand: chain 'E' and resid 75 through 81 removed outlier: 5.579A pdb=" N ALA E 76 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA E 94 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA E 78 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS E 33 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU E 127 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR E 35 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU E 125 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N GLY E 300 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU E 125 " --> pdb=" O GLY E 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 161 through 163 removed outlier: 6.497A pdb=" N LEU E 161 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA E 368 " --> pdb=" O VAL E 391 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLN E 393 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA E 370 " --> pdb=" O GLN E 393 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU E 318 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 257 " --> pdb=" O HIS E 284 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N HIS E 286 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N HIS E 259 " --> pdb=" O HIS E 286 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HIS E 230 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET E 258 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU E 232 " --> pdb=" O MET E 258 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASP E 260 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR E 192 " --> pdb=" O TYR E 231 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ASN E 233 " --> pdb=" O THR E 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 345 through 346 Processing sheet with id=AC2, first strand: chain 'F' and resid 75 through 81 removed outlier: 6.721A pdb=" N PHE F 92 " --> pdb=" O TYR F 77 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE F 79 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR F 90 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP F 129 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS F 33 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU F 127 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR F 35 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU F 125 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N GLY F 300 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU F 125 " --> pdb=" O GLY F 300 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 161 through 163 removed outlier: 6.521A pdb=" N LEU F 161 " --> pdb=" O LEU F 392 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA F 368 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLN F 393 " --> pdb=" O ALA F 368 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA F 370 " --> pdb=" O GLN F 393 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 318 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE F 257 " --> pdb=" O HIS F 284 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N HIS F 286 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N HIS F 259 " --> pdb=" O HIS F 286 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N HIS F 230 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET F 258 " --> pdb=" O HIS F 230 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU F 232 " --> pdb=" O MET F 258 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ASP F 260 " --> pdb=" O LEU F 232 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR F 192 " --> pdb=" O TYR F 231 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN F 233 " --> pdb=" O THR F 192 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 345 through 346 Processing sheet with id=AC5, first strand: chain 'G' and resid 75 through 81 removed outlier: 5.579A pdb=" N ALA G 76 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA G 94 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 78 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS G 33 " --> pdb=" O LEU G 127 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU G 127 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR G 35 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU G 125 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLY G 300 " --> pdb=" O ARG G 123 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU G 125 " --> pdb=" O GLY G 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 161 through 163 removed outlier: 6.481A pdb=" N LEU G 161 " --> pdb=" O LEU G 392 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA G 368 " --> pdb=" O VAL G 391 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLN G 393 " --> pdb=" O ALA G 368 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA G 370 " --> pdb=" O GLN G 393 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU G 318 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE G 257 " --> pdb=" O HIS G 284 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N HIS G 286 " --> pdb=" O ILE G 257 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N HIS G 259 " --> pdb=" O HIS G 286 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N HIS G 230 " --> pdb=" O ILE G 256 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET G 258 " --> pdb=" O HIS G 230 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU G 232 " --> pdb=" O MET G 258 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASP G 260 " --> pdb=" O LEU G 232 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR G 192 " --> pdb=" O TYR G 231 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ASN G 233 " --> pdb=" O THR G 192 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 345 through 346 Processing sheet with id=AC8, first strand: chain 'c' and resid 63 through 64 removed outlier: 6.649A pdb=" N VAL c 94 " --> pdb=" O ILE c 112 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP c 100 " --> pdb=" O LYS c 106 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS c 106 " --> pdb=" O ASP c 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 63 through 64 removed outlier: 6.650A pdb=" N VAL d 94 " --> pdb=" O ILE d 112 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASP d 100 " --> pdb=" O LYS d 106 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS d 106 " --> pdb=" O ASP d 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 63 through 64 removed outlier: 6.650A pdb=" N VAL b 94 " --> pdb=" O ILE b 112 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP b 100 " --> pdb=" O LYS b 106 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS b 106 " --> pdb=" O ASP b 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'h' and resid 63 through 64 removed outlier: 6.651A pdb=" N VAL h 94 " --> pdb=" O ILE h 112 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP h 100 " --> pdb=" O LYS h 106 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS h 106 " --> pdb=" O ASP h 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'e' and resid 63 through 64 removed outlier: 6.650A pdb=" N VAL e 94 " --> pdb=" O ILE e 112 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASP e 100 " --> pdb=" O LYS e 106 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS e 106 " --> pdb=" O ASP e 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'f' and resid 63 through 64 removed outlier: 6.648A pdb=" N VAL f 94 " --> pdb=" O ILE f 112 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP f 100 " --> pdb=" O LYS f 106 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYS f 106 " --> pdb=" O ASP f 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'g' and resid 63 through 64 removed outlier: 6.652A pdb=" N VAL g 94 " --> pdb=" O ILE g 112 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP g 100 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYS g 106 " --> pdb=" O ASP g 100 " (cutoff:3.500A) 1719 hydrogen bonds defined for protein. 4632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 3.56 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: 11904 1.34 - 1.46: 6585 1.46 - 1.57: 18255 1.57 - 1.69: 0 1.69 - 1.81: 320 Bond restraints: 37064 Sorted by residual: bond pdb=" CG1 ILE a 97 " pdb=" CD1 ILE a 97 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.60e+00 bond pdb=" CG1 ILE h 97 " pdb=" CD1 ILE h 97 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00 bond pdb=" CG1 ILE d 97 " pdb=" CD1 ILE d 97 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00 bond pdb=" CG1 ILE g 97 " pdb=" CD1 ILE g 97 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 bond pdb=" CG1 ILE b 97 " pdb=" CD1 ILE b 97 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 ... (remaining 37059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 49564 2.16 - 4.33: 626 4.33 - 6.49: 63 6.49 - 8.66: 0 8.66 - 10.82: 3 Bond angle restraints: 50256 Sorted by residual: angle pdb=" C SER F 53 " pdb=" N SER F 54 " pdb=" CA SER F 54 " ideal model delta sigma weight residual 121.90 116.22 5.68 1.26e+00 6.30e-01 2.03e+01 angle pdb=" C SER D 53 " pdb=" N SER D 54 " pdb=" CA SER D 54 " ideal model delta sigma weight residual 121.90 116.26 5.64 1.26e+00 6.30e-01 2.00e+01 angle pdb=" C SER H 53 " pdb=" N SER H 54 " pdb=" CA SER H 54 " ideal model delta sigma weight residual 121.90 116.28 5.62 1.26e+00 6.30e-01 1.99e+01 angle pdb=" C SER A 53 " pdb=" N SER A 54 " pdb=" CA SER A 54 " ideal model delta sigma weight residual 121.90 116.29 5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" C SER B 53 " pdb=" N SER B 54 " pdb=" CA SER B 54 " ideal model delta sigma weight residual 121.90 116.37 5.53 1.26e+00 6.30e-01 1.92e+01 ... (remaining 50251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 19740 17.90 - 35.79: 1533 35.79 - 53.69: 335 53.69 - 71.59: 91 71.59 - 89.48: 53 Dihedral angle restraints: 21752 sinusoidal: 8704 harmonic: 13048 Sorted by residual: dihedral pdb=" CA PHE C 191 " pdb=" C PHE C 191 " pdb=" N THR C 192 " pdb=" CA THR C 192 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PHE G 191 " pdb=" C PHE G 191 " pdb=" N THR G 192 " pdb=" CA THR G 192 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE A 191 " pdb=" C PHE A 191 " pdb=" N THR A 192 " pdb=" CA THR A 192 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 21749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3043 0.033 - 0.065: 1547 0.065 - 0.098: 440 0.098 - 0.131: 209 0.131 - 0.164: 33 Chirality restraints: 5272 Sorted by residual: chirality pdb=" CB ILE D 429 " pdb=" CA ILE D 429 " pdb=" CG1 ILE D 429 " pdb=" CG2 ILE D 429 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CB ILE A 429 " pdb=" CA ILE A 429 " pdb=" CG1 ILE A 429 " pdb=" CG2 ILE A 429 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CB ILE B 429 " pdb=" CA ILE B 429 " pdb=" CG1 ILE B 429 " pdb=" CG2 ILE B 429 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 5269 not shown) Planarity restraints: 6536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 201 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO B 202 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 201 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO H 202 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 202 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 202 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 201 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.50e+00 pdb=" N PRO F 202 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 202 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 202 " 0.022 5.00e-02 4.00e+02 ... (remaining 6533 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 251 2.61 - 3.18: 32035 3.18 - 3.75: 62596 3.75 - 4.33: 93913 4.33 - 4.90: 147062 Nonbonded interactions: 335857 Sorted by model distance: nonbonded pdb=" CB VAL c 14 " pdb=" NZ LYS c 116 " model vdw 2.033 3.550 nonbonded pdb=" O GLY A 171 " pdb=" NE2 GLN c 104 " model vdw 2.061 3.120 nonbonded pdb=" O GLY H 171 " pdb=" NE2 GLN e 104 " model vdw 2.062 3.120 nonbonded pdb=" O GLY E 171 " pdb=" NE2 GLN f 104 " model vdw 2.062 3.120 nonbonded pdb=" O GLY F 171 " pdb=" NE2 GLN g 104 " model vdw 2.064 3.120 ... (remaining 335852 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } 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: 8.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 27.780 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9220 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 37064 Z= 0.220 Angle : 0.597 10.824 50256 Z= 0.326 Chirality : 0.045 0.164 5272 Planarity : 0.004 0.041 6536 Dihedral : 14.838 89.484 13448 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.12), residues: 4520 helix: 1.61 (0.12), residues: 1864 sheet: -0.21 (0.18), residues: 776 loop : 0.89 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 123 TYR 0.018 0.002 TYR A 261 PHE 0.018 0.002 PHE F 303 TRP 0.018 0.001 TRP F 337 HIS 0.008 0.001 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00483 (37064) covalent geometry : angle 0.59740 (50256) hydrogen bonds : bond 0.16002 ( 1719) hydrogen bonds : angle 6.52462 ( 4632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 0.979 Fit side-chains REVERT: h 35 LYS cc_start: 0.8865 (mttp) cc_final: 0.8617 (mttp) REVERT: e 35 LYS cc_start: 0.8923 (mttp) cc_final: 0.8681 (mttp) outliers start: 0 outliers final: 0 residues processed: 617 average time/residue: 0.8135 time to fit residues: 582.3770 Evaluate side-chains 609 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.2980 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN C 115 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN d 101 ASN b 101 ASN h 101 ASN e 101 ASN f 101 ASN g 101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.111145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085733 restraints weight = 37048.223| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.23 r_work: 0.2899 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37064 Z= 0.156 Angle : 0.551 7.675 50256 Z= 0.300 Chirality : 0.043 0.146 5272 Planarity : 0.004 0.039 6536 Dihedral : 4.861 21.656 5000 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.13 % Allowed : 9.70 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.12), residues: 4520 helix: 2.06 (0.12), residues: 1832 sheet: -0.29 (0.18), residues: 784 loop : 0.99 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 123 TYR 0.014 0.002 TYR A 136 PHE 0.019 0.002 PHE G 303 TRP 0.019 0.001 TRP C 337 HIS 0.005 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00336 (37064) covalent geometry : angle 0.55091 (50256) hydrogen bonds : bond 0.04922 ( 1719) hydrogen bonds : angle 5.46627 ( 4632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 623 time to evaluate : 1.388 Fit side-chains REVERT: h 35 LYS cc_start: 0.9004 (mttp) cc_final: 0.8737 (mttp) REVERT: e 35 LYS cc_start: 0.9008 (mttp) cc_final: 0.8735 (mttp) outliers start: 42 outliers final: 22 residues processed: 631 average time/residue: 0.7921 time to fit residues: 583.8104 Evaluate side-chains 607 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 585 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain a residue 104 GLN Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain c residue 64 MET Chi-restraints excluded: chain d residue 64 MET Chi-restraints excluded: chain b residue 104 GLN Chi-restraints excluded: chain h residue 64 MET Chi-restraints excluded: chain h residue 104 GLN Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain f residue 64 MET Chi-restraints excluded: chain f residue 104 GLN Chi-restraints excluded: chain g residue 64 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 109 optimal weight: 7.9990 chunk 159 optimal weight: 0.3980 chunk 258 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 380 optimal weight: 1.9990 chunk 427 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 447 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN d 101 ASN b 101 ASN h 101 ASN e 101 ASN f 101 ASN g 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084290 restraints weight = 36995.973| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.23 r_work: 0.2868 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37064 Z= 0.198 Angle : 0.577 8.103 50256 Z= 0.314 Chirality : 0.044 0.151 5272 Planarity : 0.004 0.038 6536 Dihedral : 4.979 22.391 5000 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.75 % Allowed : 9.35 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.12), residues: 4520 helix: 2.06 (0.12), residues: 1824 sheet: -0.30 (0.18), residues: 784 loop : 0.99 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 209 TYR 0.017 0.002 TYR G 261 PHE 0.021 0.002 PHE G 303 TRP 0.019 0.001 TRP E 337 HIS 0.007 0.001 HIS G 145 Details of bonding type rmsd covalent geometry : bond 0.00433 (37064) covalent geometry : angle 0.57743 (50256) hydrogen bonds : bond 0.05204 ( 1719) hydrogen bonds : angle 5.45067 ( 4632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 614 time to evaluate : 1.072 Fit side-chains REVERT: h 35 LYS cc_start: 0.9000 (mttp) cc_final: 0.8712 (mttp) REVERT: e 35 LYS cc_start: 0.9005 (mttp) cc_final: 0.8616 (mttp) REVERT: g 35 LYS cc_start: 0.8954 (mttp) cc_final: 0.8658 (mttp) outliers start: 65 outliers final: 25 residues processed: 636 average time/residue: 0.7634 time to fit residues: 566.9691 Evaluate side-chains 612 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 587 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain a residue 104 GLN Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 164 CYS Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain b residue 104 GLN Chi-restraints excluded: chain h residue 104 GLN Chi-restraints excluded: chain f residue 104 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 280 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 420 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 430 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 343 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN d 101 ASN b 101 ASN h 101 ASN e 101 ASN f 101 ASN g 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.086446 restraints weight = 36799.012| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.23 r_work: 0.2914 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 37064 Z= 0.137 Angle : 0.526 7.412 50256 Z= 0.283 Chirality : 0.042 0.142 5272 Planarity : 0.003 0.038 6536 Dihedral : 4.775 21.487 5000 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.21 % Allowed : 9.84 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.13), residues: 4520 helix: 2.19 (0.12), residues: 1832 sheet: -0.34 (0.18), residues: 784 loop : 1.03 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.013 0.001 TYR G 261 PHE 0.017 0.002 PHE D 303 TRP 0.019 0.001 TRP C 337 HIS 0.005 0.001 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00297 (37064) covalent geometry : angle 0.52583 (50256) hydrogen bonds : bond 0.04417 ( 1719) hydrogen bonds : angle 5.30076 ( 4632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 617 time to evaluate : 1.092 Fit side-chains REVERT: F 429 ILE cc_start: 0.8117 (tp) cc_final: 0.7752 (pt) REVERT: d 116 LYS cc_start: 0.6417 (OUTLIER) cc_final: 0.6209 (ptmm) REVERT: h 35 LYS cc_start: 0.8994 (mttp) cc_final: 0.8664 (mttp) REVERT: e 35 LYS cc_start: 0.8997 (mttp) cc_final: 0.8681 (mttp) REVERT: g 35 LYS cc_start: 0.8964 (mttp) cc_final: 0.8695 (mttp) outliers start: 45 outliers final: 20 residues processed: 638 average time/residue: 0.7522 time to fit residues: 562.6378 Evaluate side-chains 608 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 587 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain H residue 164 CYS Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain d residue 116 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 263 optimal weight: 3.9990 chunk 372 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 336 optimal weight: 0.4980 chunk 139 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 93 optimal weight: 0.2980 chunk 170 optimal weight: 5.9990 chunk 384 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 354 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 101 ASN ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** c 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 ASN b 101 ASN ** b 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 101 ASN ** h 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 101 ASN ** e 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 101 ASN ** f 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 101 ASN ** g 104 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 = 0.3571 r_free = 0.3571 target = 0.115128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090314 restraints weight = 37400.645| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.24 r_work: 0.2998 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 37064 Z= 0.096 Angle : 0.478 7.599 50256 Z= 0.254 Chirality : 0.040 0.137 5272 Planarity : 0.003 0.038 6536 Dihedral : 4.455 20.261 5000 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.21 % Allowed : 10.65 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.13), residues: 4520 helix: 2.41 (0.12), residues: 1832 sheet: -0.35 (0.18), residues: 784 loop : 1.02 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 123 TYR 0.010 0.001 TYR B 261 PHE 0.011 0.001 PHE A 303 TRP 0.020 0.001 TRP B 337 HIS 0.003 0.001 HIS f 89 Details of bonding type rmsd covalent geometry : bond 0.00204 (37064) covalent geometry : angle 0.47775 (50256) hydrogen bonds : bond 0.03622 ( 1719) hydrogen bonds : angle 5.11537 ( 4632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 608 time to evaluate : 1.313 Fit side-chains REVERT: d 4 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7347 (ttt) REVERT: d 116 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6256 (ptmm) REVERT: h 35 LYS cc_start: 0.8989 (mttp) cc_final: 0.8636 (mttp) REVERT: e 35 LYS cc_start: 0.8981 (mttp) cc_final: 0.8665 (mttp) REVERT: g 4 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7382 (ttt) REVERT: g 35 LYS cc_start: 0.8974 (mttp) cc_final: 0.8670 (mttp) outliers start: 45 outliers final: 19 residues processed: 629 average time/residue: 0.7475 time to fit residues: 551.3069 Evaluate side-chains 592 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 570 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain H residue 164 CYS Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain d residue 116 LYS Chi-restraints excluded: chain g residue 4 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 418 optimal weight: 4.9990 chunk 287 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 425 optimal weight: 0.3980 chunk 343 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 101 ASN h 101 ASN f 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.112114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.086167 restraints weight = 38120.208| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.27 r_work: 0.2919 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37064 Z= 0.150 Angle : 0.536 8.021 50256 Z= 0.287 Chirality : 0.042 0.144 5272 Planarity : 0.003 0.037 6536 Dihedral : 4.718 21.504 5000 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.32 % Allowed : 10.43 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.13), residues: 4520 helix: 2.28 (0.12), residues: 1832 sheet: -0.34 (0.18), residues: 784 loop : 1.02 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 287 TYR 0.014 0.002 TYR G 261 PHE 0.018 0.002 PHE B 303 TRP 0.017 0.001 TRP E 337 HIS 0.005 0.001 HIS E 145 Details of bonding type rmsd covalent geometry : bond 0.00326 (37064) covalent geometry : angle 0.53570 (50256) hydrogen bonds : bond 0.04504 ( 1719) hydrogen bonds : angle 5.27583 ( 4632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 596 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: a 19 PHE cc_start: 0.8673 (m-80) cc_final: 0.8447 (m-80) REVERT: d 19 PHE cc_start: 0.8684 (m-80) cc_final: 0.8455 (m-80) REVERT: h 19 PHE cc_start: 0.8682 (m-80) cc_final: 0.8465 (m-80) REVERT: h 35 LYS cc_start: 0.8979 (mttp) cc_final: 0.8623 (mttp) REVERT: g 35 LYS cc_start: 0.8957 (mmtp) cc_final: 0.8626 (mttp) outliers start: 49 outliers final: 24 residues processed: 628 average time/residue: 0.7583 time to fit residues: 558.1222 Evaluate side-chains 599 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 575 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain a residue 116 LYS Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain H residue 164 CYS Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain h residue 116 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 2 optimal weight: 6.9990 chunk 383 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 420 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 406 optimal weight: 30.0000 chunk 103 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN C 115 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN d 101 ASN b 101 ASN h 101 ASN e 101 ASN f 101 ASN g 101 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.111105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.085045 restraints weight = 38151.709| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.27 r_work: 0.2895 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 37064 Z= 0.181 Angle : 0.566 8.816 50256 Z= 0.304 Chirality : 0.043 0.151 5272 Planarity : 0.004 0.037 6536 Dihedral : 4.870 22.320 5000 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.10 % Allowed : 10.30 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.13), residues: 4520 helix: 2.18 (0.12), residues: 1832 sheet: -0.35 (0.18), residues: 784 loop : 1.01 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.015 0.002 TYR C 261 PHE 0.020 0.002 PHE D 303 TRP 0.016 0.001 TRP E 337 HIS 0.006 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00395 (37064) covalent geometry : angle 0.56581 (50256) hydrogen bonds : bond 0.04859 ( 1719) hydrogen bonds : angle 5.37445 ( 4632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 600 time to evaluate : 1.326 Fit side-chains REVERT: a 19 PHE cc_start: 0.8699 (m-80) cc_final: 0.8495 (m-80) REVERT: c 19 PHE cc_start: 0.8689 (m-80) cc_final: 0.8472 (m-80) REVERT: h 19 PHE cc_start: 0.8690 (m-80) cc_final: 0.8488 (m-80) REVERT: h 35 LYS cc_start: 0.8976 (mttp) cc_final: 0.8607 (mttp) REVERT: e 35 LYS cc_start: 0.8993 (mttp) cc_final: 0.8669 (mttp) REVERT: g 35 LYS cc_start: 0.8951 (mmtp) cc_final: 0.8581 (mttp) outliers start: 41 outliers final: 20 residues processed: 621 average time/residue: 0.8054 time to fit residues: 583.7842 Evaluate side-chains 599 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 579 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain a residue 116 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain H residue 164 CYS Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain h residue 116 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 9 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 342 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 379 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 184 optimal weight: 0.3980 chunk 420 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN C 115 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN d 101 ASN d 104 GLN b 101 ASN h 101 ASN e 101 ASN f 101 ASN g 101 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083742 restraints weight = 38052.865| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.26 r_work: 0.2869 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37064 Z= 0.239 Angle : 0.614 9.412 50256 Z= 0.330 Chirality : 0.046 0.158 5272 Planarity : 0.004 0.037 6536 Dihedral : 5.034 22.746 5000 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.86 % Allowed : 10.16 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.12), residues: 4520 helix: 2.07 (0.12), residues: 1824 sheet: -0.35 (0.18), residues: 784 loop : 0.96 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG h 17 TYR 0.019 0.002 TYR C 261 PHE 0.023 0.002 PHE D 303 TRP 0.015 0.001 TRP E 337 HIS 0.008 0.001 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00524 (37064) covalent geometry : angle 0.61423 (50256) hydrogen bonds : bond 0.05393 ( 1719) hydrogen bonds : angle 5.48421 ( 4632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 597 time to evaluate : 1.462 Fit side-chains REVERT: c 19 PHE cc_start: 0.8703 (m-80) cc_final: 0.8502 (m-80) REVERT: h 35 LYS cc_start: 0.8969 (mttp) cc_final: 0.8583 (mttp) REVERT: e 35 LYS cc_start: 0.8990 (mttp) cc_final: 0.8652 (mttp) REVERT: g 35 LYS cc_start: 0.8952 (mmtp) cc_final: 0.8594 (mttp) outliers start: 32 outliers final: 17 residues processed: 615 average time/residue: 0.7849 time to fit residues: 561.0054 Evaluate side-chains 603 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 586 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain a residue 116 LYS Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain b residue 116 LYS Chi-restraints excluded: chain h residue 116 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 97 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 354 optimal weight: 7.9990 chunk 353 optimal weight: 0.7980 chunk 410 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 101 ASN h 101 ASN e 101 ASN f 101 ASN g 101 ASN g 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.111605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.085840 restraints weight = 36969.323| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.26 r_work: 0.2898 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37064 Z= 0.146 Angle : 0.544 8.647 50256 Z= 0.291 Chirality : 0.042 0.144 5272 Planarity : 0.004 0.038 6536 Dihedral : 4.826 21.831 5000 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.56 % Allowed : 10.51 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.12), residues: 4520 helix: 2.18 (0.12), residues: 1832 sheet: -0.37 (0.18), residues: 784 loop : 0.98 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.014 0.002 TYR E 261 PHE 0.018 0.002 PHE H 303 TRP 0.019 0.001 TRP H 337 HIS 0.005 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00317 (37064) covalent geometry : angle 0.54390 (50256) hydrogen bonds : bond 0.04482 ( 1719) hydrogen bonds : angle 5.31531 ( 4632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 600 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: c 19 PHE cc_start: 0.8669 (m-80) cc_final: 0.8468 (m-80) REVERT: h 35 LYS cc_start: 0.8955 (mttp) cc_final: 0.8592 (mttp) REVERT: g 35 LYS cc_start: 0.8930 (mmtp) cc_final: 0.8565 (mttp) outliers start: 21 outliers final: 20 residues processed: 609 average time/residue: 0.7842 time to fit residues: 558.1745 Evaluate side-chains 600 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 580 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain a residue 116 LYS Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain H residue 164 CYS Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain b residue 116 LYS Chi-restraints excluded: chain h residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 428 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 199 optimal weight: 0.0370 chunk 410 optimal weight: 0.8980 chunk 314 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 337 optimal weight: 4.9990 chunk 391 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN C 115 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN b 101 ASN h 101 ASN e 101 ASN f 101 ASN g 101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.111107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084942 restraints weight = 36046.021| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.27 r_work: 0.2902 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37064 Z= 0.156 Angle : 0.560 9.587 50256 Z= 0.298 Chirality : 0.043 0.146 5272 Planarity : 0.004 0.037 6536 Dihedral : 4.841 21.897 5000 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.70 % Allowed : 10.35 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.12), residues: 4520 helix: 2.15 (0.12), residues: 1832 sheet: -0.37 (0.18), residues: 784 loop : 0.97 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.014 0.002 TYR E 261 PHE 0.019 0.002 PHE A 303 TRP 0.018 0.001 TRP F 337 HIS 0.005 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00341 (37064) covalent geometry : angle 0.55975 (50256) hydrogen bonds : bond 0.04609 ( 1719) hydrogen bonds : angle 5.33857 ( 4632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 586 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 35 LYS cc_start: 0.8979 (mttp) cc_final: 0.8636 (mttp) REVERT: g 35 LYS cc_start: 0.8943 (mmtp) cc_final: 0.8589 (mttp) outliers start: 26 outliers final: 18 residues processed: 598 average time/residue: 0.7889 time to fit residues: 551.0424 Evaluate side-chains 595 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 577 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain a residue 116 LYS Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain b residue 116 LYS Chi-restraints excluded: chain h residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 399 optimal weight: 7.9990 chunk 15 optimal weight: 0.0040 chunk 107 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 overall best weight: 1.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 ASN b 101 ASN h 101 ASN e 101 ASN f 101 ASN g 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.112264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086333 restraints weight = 36763.810| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.27 r_work: 0.2933 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37064 Z= 0.140 Angle : 0.544 9.248 50256 Z= 0.289 Chirality : 0.042 0.143 5272 Planarity : 0.003 0.037 6536 Dihedral : 4.775 21.535 5000 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.54 % Allowed : 10.32 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.12), residues: 4520 helix: 2.18 (0.12), residues: 1832 sheet: -0.38 (0.18), residues: 784 loop : 0.98 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 287 TYR 0.014 0.001 TYR C 261 PHE 0.017 0.002 PHE B 303 TRP 0.019 0.001 TRP F 337 HIS 0.005 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00303 (37064) covalent geometry : angle 0.54443 (50256) hydrogen bonds : bond 0.04388 ( 1719) hydrogen bonds : angle 5.29406 ( 4632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23658.13 seconds wall clock time: 400 minutes 22.56 seconds (24022.56 seconds total)