Starting phenix.real_space_refine on Mon Jul 6 00:48:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eau_47846/07_2026/9eau_47846.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eau_47846/07_2026/9eau_47846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eau_47846/07_2026/9eau_47846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eau_47846/07_2026/9eau_47846.map" model { file = "/net/cci-nas-00/data/ceres_data/9eau_47846/07_2026/9eau_47846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eau_47846/07_2026/9eau_47846.cif" } resolution = 3.06 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= 0.002 sd= 0.144 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 236 5.16 5 C 20047 2.51 5 N 5478 2.21 5 O 6016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31779 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3325 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "B" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3257 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 32, 'TRANS': 386} Chain: "C" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1215 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "E" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3320 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3257 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 32, 'TRANS': 386} Chain: "G" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1215 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "I" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3323 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3257 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 32, 'TRANS': 386} Chain: "K" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1215 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "M" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3325 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "N" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3257 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 32, 'TRANS': 386} Chain: "O" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1215 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "Y" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "Z" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 6.05, per 1000 atoms: 0.19 Number of scatterers: 31779 At special positions: 0 Unit cell: (186.48, 183.15, 196.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 236 16.00 O 6016 8.00 N 5478 7.00 C 20047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 28 " distance=2.04 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 125 " distance=2.04 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.03 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.02 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 125 " distance=2.03 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 120 " - pdb=" SG CYS G 135 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 114 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 94 " distance=2.03 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 259 " - pdb=" SG CYS I 271 " distance=2.03 Simple disulfide: pdb=" SG CYS I 301 " - pdb=" SG CYS I 376 " distance=2.03 Simple disulfide: pdb=" SG CYS I 306 " - pdb=" SG CYS I 380 " distance=2.03 Simple disulfide: pdb=" SG CYS I 328 " - pdb=" SG CYS I 370 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.03 Simple disulfide: pdb=" SG CYS K 120 " - pdb=" SG CYS K 135 " distance=2.03 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 114 " distance=2.03 Simple disulfide: pdb=" SG CYS M 62 " - pdb=" SG CYS M 94 " distance=2.03 Simple disulfide: pdb=" SG CYS M 63 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 259 " - pdb=" SG CYS M 271 " distance=2.03 Simple disulfide: pdb=" SG CYS M 301 " - pdb=" SG CYS M 376 " distance=2.03 Simple disulfide: pdb=" SG CYS M 306 " - pdb=" SG CYS M 380 " distance=2.03 Simple disulfide: pdb=" SG CYS M 328 " - pdb=" SG CYS M 370 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 105 " distance=2.03 Simple disulfide: pdb=" SG CYS O 120 " - pdb=" SG CYS O 135 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 113 " - pdb=" SG CYS Y 127 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 120 " - pdb=" SG CYS Y 140 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 134 " - pdb=" SG CYS Y 149 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 113 " - pdb=" SG CYS Z 127 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 120 " - pdb=" SG CYS Z 140 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 134 " - pdb=" SG CYS Z 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 96 sheets defined 15.0% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 238 through 247 removed outlier: 4.185A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.027A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 438 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.857A pdb=" N ALA B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 362 through 402 Proline residue: B 398 - end of helix Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.660A pdb=" N LEU B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 121 Processing helix chain 'C' and resid 177 through 181 removed outlier: 4.206A pdb=" N SER C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 removed outlier: 4.042A pdb=" N LYS E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 255 through 259 removed outlier: 4.061A pdb=" N GLY E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 404 through 438 Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.618A pdb=" N ASN F 7 " --> pdb=" O THR F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 12 removed outlier: 3.987A pdb=" N ALA F 11 " --> pdb=" O VAL F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 350 through 361 removed outlier: 3.717A pdb=" N LEU F 361 " --> pdb=" O TYR F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 402 Proline residue: F 398 - end of helix Processing helix chain 'F' and resid 408 through 415 Processing helix chain 'G' and resid 112 through 120 removed outlier: 4.226A pdb=" N ILE G 116 " --> pdb=" O MET G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 158 Processing helix chain 'G' and resid 175 through 181 removed outlier: 3.614A pdb=" N SER G 180 " --> pdb=" O HIS G 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 247 removed outlier: 3.889A pdb=" N LYS I 245 " --> pdb=" O LYS I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 254 Processing helix chain 'I' and resid 255 through 259 removed outlier: 4.093A pdb=" N GLY I 258 " --> pdb=" O ALA I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 404 through 438 removed outlier: 3.998A pdb=" N MET I 436 " --> pdb=" O THR I 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.688A pdb=" N ALA J 11 " --> pdb=" O VAL J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'J' and resid 350 through 361 removed outlier: 3.737A pdb=" N LEU J 361 " --> pdb=" O TYR J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 402 Proline residue: J 398 - end of helix Processing helix chain 'J' and resid 408 through 415 Processing helix chain 'K' and resid 113 through 120 removed outlier: 4.476A pdb=" N ASP K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 158 Processing helix chain 'K' and resid 177 through 181 Processing helix chain 'M' and resid 238 through 247 removed outlier: 4.124A pdb=" N LYS M 245 " --> pdb=" O LYS M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 254 Processing helix chain 'M' and resid 255 through 259 removed outlier: 4.174A pdb=" N GLY M 258 " --> pdb=" O ALA M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 287 Processing helix chain 'M' and resid 404 through 438 Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 8 through 10 No H-bonds generated for 'chain 'N' and resid 8 through 10' Processing helix chain 'N' and resid 81 through 83 No H-bonds generated for 'chain 'N' and resid 81 through 83' Processing helix chain 'N' and resid 350 through 361 removed outlier: 3.857A pdb=" N LEU N 361 " --> pdb=" O TYR N 357 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 402 Proline residue: N 398 - end of helix Processing helix chain 'N' and resid 408 through 416 removed outlier: 3.864A pdb=" N LEU N 414 " --> pdb=" O THR N 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 120 Processing helix chain 'O' and resid 153 through 158 Processing helix chain 'O' and resid 177 through 181 Processing helix chain 'Y' and resid 131 through 133 No H-bonds generated for 'chain 'Y' and resid 131 through 133' Processing helix chain 'Z' and resid 131 through 133 No H-bonds generated for 'chain 'Z' and resid 131 through 133' Processing helix chain 'Z' and resid 142 through 146 removed outlier: 3.618A pdb=" N ASP Z 145 " --> pdb=" O SER Z 142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 6.435A pdb=" N THR A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR A 36 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A 42 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA A 124 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR A 46 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 4.832A pdb=" N SER A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR A 46 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA A 124 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A 42 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR A 36 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'A' and resid 297 through 306 removed outlier: 4.112A pdb=" N LEU A 299 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER A 319 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N CYS A 301 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 317 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL A 303 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL A 315 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain 'B' and resid 34 through 38 removed outlier: 8.625A pdb=" N ILE B 34 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER B 51 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N SER B 51 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET B 70 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS B 66 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 34 through 38 removed outlier: 8.625A pdb=" N ILE B 34 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER B 51 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N HIS B 99 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ALA B 52 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N MET B 97 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N ILE B 54 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N GLY B 95 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 15.383A pdb=" N LEU B 56 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 18.721A pdb=" N ILE B 93 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.441A pdb=" N ASP B 109 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 149 through 156 Processing sheet with id=AB7, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AB8, first strand: chain 'B' and resid 175 through 176 removed outlier: 5.754A pdb=" N ILE B 197 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AC1, first strand: chain 'B' and resid 274 through 278 Processing sheet with id=AC2, first strand: chain 'C' and resid 129 through 133 removed outlier: 5.248A pdb=" N VAL C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU C 126 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 132 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 135 through 137 removed outlier: 3.510A pdb=" N CYS C 135 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 192 through 196 removed outlier: 3.701A pdb=" N TRP C 196 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ALA C 200 " --> pdb=" O PRO C 211 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE C 208 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARG C 244 " --> pdb=" O ASN C 240 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN C 240 " --> pdb=" O ARG C 244 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA C 246 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY C 238 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N SER C 248 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 224 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AC6, first strand: chain 'E' and resid 14 through 19 removed outlier: 6.463A pdb=" N THR E 132 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR E 36 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS E 130 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU E 38 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER E 128 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR E 126 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU E 42 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA E 124 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 44 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 122 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR E 46 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER E 120 " --> pdb=" O TYR E 46 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 140 through 147 removed outlier: 4.823A pdb=" N SER E 120 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR E 46 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 122 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 44 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA E 124 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU E 42 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR E 126 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER E 128 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU E 38 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS E 130 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR E 36 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR E 132 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AD1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'E' and resid 203 through 205 Processing sheet with id=AD3, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'E' and resid 297 through 306 removed outlier: 5.221A pdb=" N ASP E 298 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS E 321 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL E 315 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AD6, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AD7, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AD8, first strand: chain 'F' and resid 34 through 38 removed outlier: 8.413A pdb=" N ILE F 34 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER F 51 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS F 36 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N SER F 51 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N MET F 70 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS F 66 " --> pdb=" O GLY F 55 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 34 through 38 removed outlier: 8.413A pdb=" N ILE F 34 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER F 51 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS F 36 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N HIS F 99 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ALA F 52 " --> pdb=" O MET F 97 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N MET F 97 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N ILE F 54 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N GLY F 95 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 15.278A pdb=" N LEU F 56 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 18.670A pdb=" N ILE F 93 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 84 through 86 removed outlier: 3.518A pdb=" N TYR F 110 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR F 129 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS F 112 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL F 127 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N SER F 114 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N CYS F 125 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU F 116 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS F 123 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 149 through 156 Processing sheet with id=AE3, first strand: chain 'F' and resid 236 through 237 Processing sheet with id=AE4, first strand: chain 'F' and resid 175 through 176 removed outlier: 5.711A pdb=" N ILE F 197 " --> pdb=" O GLY F 209 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 181 through 184 Processing sheet with id=AE6, first strand: chain 'F' and resid 274 through 278 Processing sheet with id=AE7, first strand: chain 'G' and resid 150 through 151 removed outlier: 3.630A pdb=" N GLY G 132 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU G 126 " --> pdb=" O VAL G 130 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL G 130 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR G 133 " --> pdb=" O PRO G 144 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA G 172 " --> pdb=" O VAL G 141 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 192 through 194 Processing sheet with id=AE9, first strand: chain 'G' and resid 223 through 225 removed outlier: 6.632A pdb=" N ILE G 224 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA G 233 " --> pdb=" O TRP G 252 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N TRP G 252 " --> pdb=" O ALA G 233 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL G 235 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL G 250 " --> pdb=" O VAL G 235 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 223 through 225 removed outlier: 6.632A pdb=" N ILE G 224 " --> pdb=" O VAL G 232 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 2 through 8 removed outlier: 3.712A pdb=" N LYS I 160 " --> pdb=" O ASP I 281 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 14 through 19 removed outlier: 6.471A pdb=" N THR I 132 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR I 36 " --> pdb=" O LYS I 130 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS I 130 " --> pdb=" O THR I 36 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU I 38 " --> pdb=" O SER I 128 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N SER I 128 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR I 126 " --> pdb=" O PRO I 40 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU I 42 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA I 124 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU I 44 " --> pdb=" O TYR I 122 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR I 122 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR I 46 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER I 120 " --> pdb=" O TYR I 46 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 140 through 147 removed outlier: 4.861A pdb=" N SER I 120 " --> pdb=" O TYR I 46 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR I 46 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR I 122 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU I 44 " --> pdb=" O TYR I 122 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA I 124 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU I 42 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR I 126 " --> pdb=" O PRO I 40 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N SER I 128 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU I 38 " --> pdb=" O SER I 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS I 130 " --> pdb=" O THR I 36 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR I 36 " --> pdb=" O LYS I 130 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR I 132 " --> pdb=" O VAL I 34 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AF6, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=AF7, first strand: chain 'I' and resid 203 through 205 Processing sheet with id=AF8, first strand: chain 'I' and resid 220 through 221 Processing sheet with id=AF9, first strand: chain 'I' and resid 297 through 306 removed outlier: 5.345A pdb=" N ASP I 298 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS I 321 " --> pdb=" O ASP I 298 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL I 315 " --> pdb=" O VAL I 304 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 343 through 346 removed outlier: 3.555A pdb=" N HIS I 331 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 387 through 388 Processing sheet with id=AG3, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AG4, first strand: chain 'J' and resid 34 through 38 removed outlier: 8.560A pdb=" N ILE J 34 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER J 51 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS J 36 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N SER J 51 " --> pdb=" O MET J 70 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET J 70 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS J 66 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 34 through 38 removed outlier: 8.560A pdb=" N ILE J 34 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER J 51 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS J 36 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N HIS J 99 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ALA J 52 " --> pdb=" O MET J 97 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N MET J 97 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ILE J 54 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 10.404A pdb=" N GLY J 95 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 15.444A pdb=" N LEU J 56 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 18.751A pdb=" N ILE J 93 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 84 through 86 removed outlier: 4.567A pdb=" N ASP J 109 " --> pdb=" O TYR J 129 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 149 through 156 Processing sheet with id=AG8, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AG9, first strand: chain 'J' and resid 175 through 176 Processing sheet with id=AH1, first strand: chain 'J' and resid 181 through 184 Processing sheet with id=AH2, first strand: chain 'J' and resid 276 through 278 Processing sheet with id=AH3, first strand: chain 'K' and resid 150 through 151 removed outlier: 6.586A pdb=" N PHE K 122 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR K 133 " --> pdb=" O PHE K 122 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL K 124 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA K 172 " --> pdb=" O VAL K 141 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 193 through 195 Processing sheet with id=AH5, first strand: chain 'K' and resid 223 through 225 removed outlier: 6.830A pdb=" N ILE K 224 " --> pdb=" O VAL K 232 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL K 232 " --> pdb=" O TRP K 252 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TRP K 252 " --> pdb=" O VAL K 232 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR K 251 " --> pdb=" O THR K 258 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 246 through 247 removed outlier: 3.571A pdb=" N ALA K 246 " --> pdb=" O ALA K 239 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 2 through 8 removed outlier: 3.714A pdb=" N LYS M 160 " --> pdb=" O ASP M 281 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 14 through 19 removed outlier: 3.502A pdb=" N TYR M 15 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU M 29 " --> pdb=" O TYR M 137 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR M 137 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU M 31 " --> pdb=" O ILE M 135 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE M 135 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL M 33 " --> pdb=" O ILE M 133 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE M 133 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU M 35 " --> pdb=" O ALA M 131 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA M 131 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER M 37 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU M 129 " --> pdb=" O SER M 37 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU M 39 " --> pdb=" O ALA M 127 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA M 127 " --> pdb=" O GLU M 39 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA M 121 " --> pdb=" O GLU M 45 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE M 47 " --> pdb=" O ALA M 119 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA M 119 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 140 through 147 removed outlier: 6.595A pdb=" N ALA M 119 " --> pdb=" O ILE M 47 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE M 47 " --> pdb=" O ALA M 119 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA M 121 " --> pdb=" O GLU M 45 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA M 127 " --> pdb=" O GLU M 39 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU M 39 " --> pdb=" O ALA M 127 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU M 129 " --> pdb=" O SER M 37 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER M 37 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA M 131 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU M 35 " --> pdb=" O ALA M 131 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE M 133 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL M 33 " --> pdb=" O ILE M 133 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE M 135 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU M 31 " --> pdb=" O ILE M 135 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR M 137 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU M 29 " --> pdb=" O TYR M 137 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 24 through 25 removed outlier: 4.678A pdb=" N THR M 288 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 51 through 54 Processing sheet with id=AI3, first strand: chain 'M' and resid 51 through 54 Processing sheet with id=AI4, first strand: chain 'M' and resid 87 through 88 Processing sheet with id=AI5, first strand: chain 'M' and resid 203 through 205 Processing sheet with id=AI6, first strand: chain 'M' and resid 220 through 221 Processing sheet with id=AI7, first strand: chain 'M' and resid 297 through 306 removed outlier: 4.142A pdb=" N LEU M 299 " --> pdb=" O SER M 319 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER M 319 " --> pdb=" O LEU M 299 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N CYS M 301 " --> pdb=" O THR M 317 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR M 317 " --> pdb=" O CYS M 301 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL M 303 " --> pdb=" O VAL M 315 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL M 315 " --> pdb=" O VAL M 303 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'M' and resid 343 through 346 Processing sheet with id=AI9, first strand: chain 'M' and resid 387 through 388 Processing sheet with id=AJ1, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.551A pdb=" N ALA N 17 " --> pdb=" O SER N 30 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 34 through 38 removed outlier: 8.522A pdb=" N ILE N 34 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER N 51 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS N 36 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N SER N 51 " --> pdb=" O MET N 70 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N MET N 70 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS N 66 " --> pdb=" O GLY N 55 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 34 through 38 removed outlier: 8.522A pdb=" N ILE N 34 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER N 51 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS N 36 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS N 99 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N ALA N 52 " --> pdb=" O MET N 97 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N MET N 97 " --> pdb=" O ALA N 52 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ILE N 54 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N GLY N 95 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 15.249A pdb=" N LEU N 56 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 18.736A pdb=" N ILE N 93 " --> pdb=" O LEU N 56 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'N' and resid 84 through 86 removed outlier: 4.434A pdb=" N ASP N 109 " --> pdb=" O TYR N 129 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'N' and resid 149 through 156 Processing sheet with id=AJ6, first strand: chain 'N' and resid 236 through 237 Processing sheet with id=AJ7, first strand: chain 'N' and resid 175 through 176 removed outlier: 4.081A pdb=" N THR N 196 " --> pdb=" O THR N 230 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'N' and resid 181 through 183 removed outlier: 3.534A pdb=" N ASP N 214 " --> pdb=" O ILE N 190 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'N' and resid 274 through 278 Processing sheet with id=AK1, first strand: chain 'O' and resid 150 through 151 removed outlier: 6.146A pdb=" N LEU O 126 " --> pdb=" O VAL O 130 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL O 130 " --> pdb=" O LEU O 126 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N TYR O 133 " --> pdb=" O PRO O 144 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'O' and resid 193 through 196 Processing sheet with id=AK3, first strand: chain 'O' and resid 223 through 225 removed outlier: 6.768A pdb=" N ILE O 224 " --> pdb=" O VAL O 232 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA O 233 " --> pdb=" O TRP O 252 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TRP O 252 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL O 235 " --> pdb=" O VAL O 250 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL O 250 " --> pdb=" O VAL O 235 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY O 237 " --> pdb=" O SER O 248 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'O' and resid 223 through 225 removed outlier: 6.768A pdb=" N ILE O 224 " --> pdb=" O VAL O 232 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Y' and resid 117 through 119 Processing sheet with id=AK6, first strand: chain 'Z' and resid 117 through 119 1231 hydrogen bonds defined for protein. 3162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5579 1.32 - 1.45: 8513 1.45 - 1.57: 18200 1.57 - 1.70: 0 1.70 - 1.82: 308 Bond restraints: 32600 Sorted by residual: bond pdb=" N VAL B 242 " pdb=" CA VAL B 242 " ideal model delta sigma weight residual 1.454 1.489 -0.035 7.70e-03 1.69e+04 2.04e+01 bond pdb=" N VAL N 242 " pdb=" CA VAL N 242 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.00e-03 1.23e+04 1.60e+01 bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.46e-02 4.69e+03 1.51e+01 bond pdb=" N ILE K 234 " pdb=" CA ILE K 234 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N VAL K 249 " pdb=" CA VAL K 249 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.80e+00 ... (remaining 32595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 42873 1.86 - 3.72: 1423 3.72 - 5.58: 94 5.58 - 7.44: 5 7.44 - 9.30: 4 Bond angle restraints: 44399 Sorted by residual: angle pdb=" N ASP M 323 " pdb=" CA ASP M 323 " pdb=" C ASP M 323 " ideal model delta sigma weight residual 114.31 105.28 9.03 1.29e+00 6.01e-01 4.90e+01 angle pdb=" CA VAL B 242 " pdb=" C VAL B 242 " pdb=" O VAL B 242 " ideal model delta sigma weight residual 119.94 117.40 2.54 5.20e-01 3.70e+00 2.38e+01 angle pdb=" CA HIS A 230 " pdb=" CB HIS A 230 " pdb=" CG HIS A 230 " ideal model delta sigma weight residual 113.80 118.63 -4.83 1.00e+00 1.00e+00 2.33e+01 angle pdb=" CA HIS F 146 " pdb=" CB HIS F 146 " pdb=" CG HIS F 146 " ideal model delta sigma weight residual 113.80 118.48 -4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" N ARG A 223 " pdb=" CA ARG A 223 " pdb=" C ARG A 223 " ideal model delta sigma weight residual 109.64 115.37 -5.73 1.27e+00 6.20e-01 2.04e+01 ... (remaining 44394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 18260 17.94 - 35.87: 1103 35.87 - 53.81: 174 53.81 - 71.75: 55 71.75 - 89.68: 26 Dihedral angle restraints: 19618 sinusoidal: 7634 harmonic: 11984 Sorted by residual: dihedral pdb=" CB CYS C 120 " pdb=" SG CYS C 120 " pdb=" SG CYS C 135 " pdb=" CB CYS C 135 " ideal model delta sinusoidal sigma weight residual 93.00 152.24 -59.24 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS G 120 " pdb=" SG CYS G 120 " pdb=" SG CYS G 135 " pdb=" CB CYS G 135 " ideal model delta sinusoidal sigma weight residual 93.00 146.30 -53.30 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA TYR I 320 " pdb=" C TYR I 320 " pdb=" N LYS I 321 " pdb=" CA LYS I 321 " ideal model delta harmonic sigma weight residual 180.00 150.79 29.21 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 19615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4184 0.068 - 0.135: 705 0.135 - 0.203: 77 0.203 - 0.270: 8 0.270 - 0.338: 1 Chirality restraints: 4975 Sorted by residual: chirality pdb=" CA VAL A 229 " pdb=" N VAL A 229 " pdb=" C VAL A 229 " pdb=" CB VAL A 229 " both_signs ideal model delta sigma weight residual False 2.44 2.78 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA VAL M 229 " pdb=" N VAL M 229 " pdb=" C VAL M 229 " pdb=" CB VAL M 229 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA VAL E 229 " pdb=" N VAL E 229 " pdb=" C VAL E 229 " pdb=" CB VAL E 229 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 4972 not shown) Planarity restraints: 5721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 110 " -0.016 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR J 110 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR J 110 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR J 110 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR J 110 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR J 110 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR J 110 " 0.029 2.00e-02 2.50e+03 pdb=" OH TYR J 110 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 222 " -0.259 9.50e-02 1.11e+02 1.16e-01 8.30e+00 pdb=" NE ARG G 222 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG G 222 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG G 222 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 222 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 46 " -0.003 2.00e-02 2.50e+03 2.04e-02 8.29e+00 pdb=" CG TYR E 46 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR E 46 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 46 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR E 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 46 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR E 46 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR E 46 " -0.029 2.00e-02 2.50e+03 ... (remaining 5718 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 292 2.62 - 3.19: 28024 3.19 - 3.76: 47145 3.76 - 4.33: 69082 4.33 - 4.90: 114916 Nonbonded interactions: 259459 Sorted by model distance: nonbonded pdb=" OH TYR N 69 " pdb=" OD1 ASP N 117 " model vdw 2.051 3.040 nonbonded pdb=" OH TYR J 69 " pdb=" OD1 ASP J 117 " model vdw 2.061 3.040 nonbonded pdb=" OH TYR B 69 " pdb=" OD1 ASP B 117 " model vdw 2.064 3.040 nonbonded pdb=" OH TYR F 69 " pdb=" OD1 ASP F 117 " model vdw 2.075 3.040 nonbonded pdb=" OD1 ASP Z 135 " pdb="CA CA Z 201 " model vdw 2.130 3.250 ... (remaining 259454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 117 or (resid 118 through 119 and (name N or nam \ e CA or name C or name O or name CB )) or resid 120 through 207 or (resid 208 an \ d (name N or name CA or name C or name O or name CB )) or resid 209 through 438) \ ) selection = (chain 'E' and (resid 1 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 438)) selection = (chain 'I' and (resid 1 through 117 or (resid 118 through 119 and (name N or nam \ e CA or name C or name O or name CB )) or resid 120 through 438)) selection = (chain 'M' and (resid 1 through 117 or (resid 118 through 119 and (name N or nam \ e CA or name C or name O or name CB )) or resid 120 through 207 or (resid 208 an \ d (name N or name CA or name C or name O or name CB )) or resid 209 through 438) \ ) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'Y' selection = chain 'Z' } 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: 2.140 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: 0.050 Extract box with map and model: 0.530 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.110 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.004 0.057 32649 Z= 0.245 Angle : 0.735 9.304 44497 Z= 0.448 Chirality : 0.051 0.338 4975 Planarity : 0.007 0.116 5721 Dihedral : 12.613 89.684 11791 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.28 % Favored : 94.55 % Rotamer: Outliers : 2.00 % Allowed : 4.15 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.12), residues: 4110 helix: -0.62 (0.21), residues: 474 sheet: -0.11 (0.15), residues: 1180 loop : -0.71 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG F 271 TYR 0.038 0.005 TYR J 110 PHE 0.019 0.002 PHE J 313 TRP 0.032 0.002 TRP C 268 HIS 0.012 0.001 HIS F 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.24 (32600) covalent geometry : angle 0.73286 / 0.45 (44399) SS BOND : bond 0.00290 / 0.18 ( 49) SS BOND : angle 1.47742 / 1.00 ( 98) hydrogen bonds : bond 0.16047 / 10.65 ( 1185) hydrogen bonds : angle 8.04725 / 5.64 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 664 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8859 (t) cc_final: 0.8633 (p) REVERT: A 14 PRO cc_start: 0.8386 (Cg_endo) cc_final: 0.8145 (Cg_exo) REVERT: A 97 ASP cc_start: 0.7796 (p0) cc_final: 0.7555 (p0) REVERT: A 130 LYS cc_start: 0.8415 (ttpp) cc_final: 0.8021 (tttt) REVERT: A 137 TYR cc_start: 0.8436 (p90) cc_final: 0.8102 (p90) REVERT: A 160 LYS cc_start: 0.8328 (mttt) cc_final: 0.7965 (mttp) REVERT: A 267 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8370 (ptt-90) REVERT: A 347 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8146 (mttp) REVERT: A 366 LYS cc_start: 0.8238 (ptmt) cc_final: 0.7571 (pttt) REVERT: A 396 ASN cc_start: 0.8776 (t0) cc_final: 0.8573 (t0) REVERT: A 397 GLN cc_start: 0.8234 (tt0) cc_final: 0.8029 (tt0) REVERT: A 436 MET cc_start: 0.7011 (tpp) cc_final: 0.6767 (mmm) REVERT: B 120 SER cc_start: 0.8072 (m) cc_final: 0.7824 (t) REVERT: B 130 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8744 (tptp) REVERT: B 142 VAL cc_start: 0.4421 (OUTLIER) cc_final: 0.3902 (t) REVERT: B 203 CYS cc_start: 0.3391 (OUTLIER) cc_final: 0.3075 (p) REVERT: B 265 CYS cc_start: 0.8163 (t) cc_final: 0.7532 (m) REVERT: B 285 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7255 (mmm160) REVERT: B 315 GLU cc_start: 0.8543 (tt0) cc_final: 0.8314 (tt0) REVERT: E 79 LYS cc_start: 0.8226 (mttt) cc_final: 0.7852 (tptm) REVERT: E 145 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8180 (mp0) REVERT: E 341 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: E 345 LYS cc_start: 0.8576 (mttt) cc_final: 0.8327 (mtpt) REVERT: E 366 LYS cc_start: 0.8752 (mtpt) cc_final: 0.7762 (ttpp) REVERT: E 401 ASP cc_start: 0.8113 (t70) cc_final: 0.7616 (t0) REVERT: E 402 MET cc_start: 0.8447 (mmt) cc_final: 0.8014 (mmt) REVERT: F 36 LYS cc_start: 0.8606 (tttp) cc_final: 0.8160 (ttmt) REVERT: F 40 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: F 70 MET cc_start: 0.8850 (mmm) cc_final: 0.8488 (mmt) REVERT: F 97 MET cc_start: 0.8840 (ttt) cc_final: 0.8631 (ttt) REVERT: F 120 SER cc_start: 0.8062 (m) cc_final: 0.7567 (p) REVERT: F 222 ILE cc_start: 0.7533 (mm) cc_final: 0.7319 (mt) REVERT: F 250 ARG cc_start: 0.8516 (ptt90) cc_final: 0.7914 (ptt180) REVERT: F 285 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7782 (mtp180) REVERT: F 346 LYS cc_start: 0.8084 (ttmm) cc_final: 0.7861 (ttmm) REVERT: F 353 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7168 (mt-10) REVERT: G 186 THR cc_start: 0.7772 (t) cc_final: 0.7530 (m) REVERT: I 7 ILE cc_start: 0.8279 (pt) cc_final: 0.7947 (pt) REVERT: I 79 LYS cc_start: 0.8135 (mttt) cc_final: 0.7668 (mmmt) REVERT: I 147 PHE cc_start: 0.8352 (m-80) cc_final: 0.8034 (m-10) REVERT: I 160 LYS cc_start: 0.8230 (mttt) cc_final: 0.7930 (mmmt) REVERT: I 264 ASN cc_start: 0.9145 (t0) cc_final: 0.8917 (t0) REVERT: I 351 LYS cc_start: 0.7598 (pttp) cc_final: 0.7235 (mtpt) REVERT: I 366 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7637 (mtpp) REVERT: I 373 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8396 (mtpp) REVERT: J 4 GLU cc_start: 0.8353 (tt0) cc_final: 0.7590 (tp30) REVERT: J 28 CYS cc_start: 0.8009 (t) cc_final: 0.7359 (p) REVERT: J 70 MET cc_start: 0.8589 (mmm) cc_final: 0.8224 (mmm) REVERT: J 79 LYS cc_start: 0.8319 (mttt) cc_final: 0.7906 (mtmm) REVERT: J 97 MET cc_start: 0.8927 (ttt) cc_final: 0.8535 (ttp) REVERT: J 110 TYR cc_start: 0.5374 (m-80) cc_final: 0.3946 (m-80) REVERT: J 120 SER cc_start: 0.7817 (m) cc_final: 0.7446 (t) REVERT: J 169 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.7497 (mpt) REVERT: J 298 SER cc_start: 0.9121 (t) cc_final: 0.8761 (m) REVERT: J 376 MET cc_start: 0.7523 (mmm) cc_final: 0.7012 (ttt) REVERT: J 390 THR cc_start: 0.7247 (m) cc_final: 0.6975 (m) REVERT: J 393 ARG cc_start: 0.5517 (ttp-170) cc_final: 0.5122 (mtp-110) REVERT: K 163 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7260 (pttp) REVERT: M 3 HIS cc_start: 0.7894 (t-90) cc_final: 0.7643 (t-170) REVERT: M 79 LYS cc_start: 0.8543 (mttt) cc_final: 0.8000 (mtpp) REVERT: M 115 LYS cc_start: 0.8927 (tttt) cc_final: 0.8619 (ttpp) REVERT: M 142 GLN cc_start: 0.8138 (tt0) cc_final: 0.7631 (tt0) REVERT: M 145 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8485 (mp0) REVERT: M 341 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: M 347 LYS cc_start: 0.8179 (mmmm) cc_final: 0.7876 (mmtp) REVERT: M 373 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8347 (mtpt) REVERT: M 384 LYS cc_start: 0.8348 (mmtm) cc_final: 0.7935 (mmtt) REVERT: M 397 GLN cc_start: 0.8726 (tt0) cc_final: 0.8386 (tt0) REVERT: M 402 MET cc_start: 0.8740 (mmt) cc_final: 0.8452 (mmm) REVERT: N 76 GLN cc_start: 0.8368 (mt0) cc_final: 0.8036 (mm-40) REVERT: N 221 LYS cc_start: 0.7387 (mmtp) cc_final: 0.6957 (mtmt) REVERT: O 179 LYS cc_start: 0.7055 (mtmt) cc_final: 0.6449 (tptt) outliers start: 70 outliers final: 19 residues processed: 710 average time/residue: 0.2247 time to fit residues: 244.0462 Evaluate side-chains 493 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 464 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 135 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS B 236 GLN B 331 ASN C 198 HIS E 102 GLN E 333 HIS F 104 HIS ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN F 331 ASN G 195 ASN G 197 HIS ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 ASN I 335 ASN J 99 HIS J 104 HIS J 236 GLN M 22 ASN M 102 GLN M 155 ASN ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 HIS N 62 HIS N 104 HIS N 236 GLN N 287 HIS Y 138 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.164019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114747 restraints weight = 36452.821| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.87 r_work: 0.3091 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 32649 Z= 0.129 Angle : 0.610 9.309 44497 Z= 0.327 Chirality : 0.046 0.238 4975 Planarity : 0.004 0.046 5721 Dihedral : 6.724 63.199 4531 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 2.46 % Allowed : 7.92 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4110 helix: 1.23 (0.23), residues: 452 sheet: 0.16 (0.15), residues: 1154 loop : -0.37 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 13 TYR 0.025 0.002 TYR F 199 PHE 0.013 0.001 PHE M 59 TRP 0.019 0.001 TRP K 268 HIS 0.009 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (32600) covalent geometry : angle 0.60706 / 0.33 (44399) SS BOND : bond 0.00815 / 0.34 ( 49) SS BOND : angle 1.45469 / 0.84 ( 98) hydrogen bonds : bond 0.03738 / 2.51 ( 1185) hydrogen bonds : angle 5.92346 / 4.17 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 502 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8665 (t) cc_final: 0.8220 (m) REVERT: A 130 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7644 (tttp) REVERT: A 160 LYS cc_start: 0.7786 (mttt) cc_final: 0.7545 (mttp) REVERT: A 171 SER cc_start: 0.8564 (p) cc_final: 0.8305 (t) REVERT: A 187 GLN cc_start: 0.8746 (tt0) cc_final: 0.8502 (tt0) REVERT: A 347 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8055 (mttp) REVERT: A 366 LYS cc_start: 0.7803 (ptmt) cc_final: 0.7010 (pttt) REVERT: A 396 ASN cc_start: 0.8718 (t0) cc_final: 0.8450 (t0) REVERT: A 397 GLN cc_start: 0.7967 (tt0) cc_final: 0.7612 (tt0) REVERT: A 402 MET cc_start: 0.7783 (mmt) cc_final: 0.7156 (mmt) REVERT: A 436 MET cc_start: 0.7035 (tpp) cc_final: 0.6819 (mmm) REVERT: B 36 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7782 (ttpp) REVERT: B 58 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7867 (mtmt) REVERT: B 61 THR cc_start: 0.8357 (m) cc_final: 0.8013 (t) REVERT: B 120 SER cc_start: 0.7786 (m) cc_final: 0.7490 (t) REVERT: B 142 VAL cc_start: 0.3267 (OUTLIER) cc_final: 0.2954 (t) REVERT: B 199 TYR cc_start: 0.7933 (p90) cc_final: 0.7548 (p90) REVERT: B 203 CYS cc_start: 0.4404 (OUTLIER) cc_final: 0.4036 (p) REVERT: B 214 ASP cc_start: 0.6346 (m-30) cc_final: 0.5432 (t0) REVERT: B 215 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7835 (ttpt) REVERT: B 222 ILE cc_start: 0.8178 (mm) cc_final: 0.7858 (mm) REVERT: B 265 CYS cc_start: 0.8243 (t) cc_final: 0.7807 (m) REVERT: B 285 ARG cc_start: 0.7690 (mtt180) cc_final: 0.6523 (mmm160) REVERT: B 315 GLU cc_start: 0.8633 (tt0) cc_final: 0.8367 (tt0) REVERT: C 112 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.4232 (tmm) REVERT: C 114 MET cc_start: 0.6520 (mpt) cc_final: 0.6106 (mpt) REVERT: C 162 LYS cc_start: 0.6708 (mtpt) cc_final: 0.6293 (ttpp) REVERT: E 79 LYS cc_start: 0.8249 (mttt) cc_final: 0.7539 (tptm) REVERT: E 115 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8481 (mtmm) REVERT: E 145 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8049 (mp0) REVERT: E 321 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7651 (mttm) REVERT: E 341 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: E 345 LYS cc_start: 0.8543 (mttt) cc_final: 0.8111 (tptp) REVERT: E 366 LYS cc_start: 0.8679 (mtpt) cc_final: 0.7598 (ttpp) REVERT: E 401 ASP cc_start: 0.7970 (t70) cc_final: 0.7530 (t0) REVERT: E 402 MET cc_start: 0.8046 (mmt) cc_final: 0.7560 (mmt) REVERT: F 4 GLU cc_start: 0.7851 (pt0) cc_final: 0.7195 (pm20) REVERT: F 36 LYS cc_start: 0.8583 (tttp) cc_final: 0.8094 (ttmt) REVERT: F 70 MET cc_start: 0.8854 (mmm) cc_final: 0.8588 (mmt) REVERT: F 120 SER cc_start: 0.7839 (m) cc_final: 0.7409 (p) REVERT: F 250 ARG cc_start: 0.8520 (ptt90) cc_final: 0.8122 (ptt180) REVERT: F 353 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7108 (mt-10) REVERT: I 7 ILE cc_start: 0.7822 (pt) cc_final: 0.7511 (pt) REVERT: I 79 LYS cc_start: 0.7904 (mttt) cc_final: 0.7318 (mmmt) REVERT: I 147 PHE cc_start: 0.8129 (m-80) cc_final: 0.7788 (m-10) REVERT: I 264 ASN cc_start: 0.8994 (t0) cc_final: 0.8759 (m110) REVERT: I 366 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7150 (ttpt) REVERT: J 4 GLU cc_start: 0.8441 (tt0) cc_final: 0.7599 (tp30) REVERT: J 28 CYS cc_start: 0.7902 (t) cc_final: 0.6994 (p) REVERT: J 32 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8027 (p) REVERT: J 70 MET cc_start: 0.8533 (mmm) cc_final: 0.8169 (mmm) REVERT: J 79 LYS cc_start: 0.8409 (mttt) cc_final: 0.8004 (mttp) REVERT: J 169 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.7318 (mpt) REVERT: J 250 ARG cc_start: 0.8567 (ptt90) cc_final: 0.8275 (ptt-90) REVERT: J 298 SER cc_start: 0.9124 (t) cc_final: 0.8812 (m) REVERT: J 376 MET cc_start: 0.7424 (mmm) cc_final: 0.6925 (ttt) REVERT: J 393 ARG cc_start: 0.5026 (ttp-170) cc_final: 0.4669 (mtp-110) REVERT: K 114 MET cc_start: 0.6269 (mpt) cc_final: 0.6017 (ptt) REVERT: K 163 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6307 (pttp) REVERT: M 3 HIS cc_start: 0.7844 (t-90) cc_final: 0.7621 (t-170) REVERT: M 75 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8826 (t0) REVERT: M 79 LYS cc_start: 0.8409 (mttt) cc_final: 0.7474 (mmmt) REVERT: M 115 LYS cc_start: 0.8938 (tttt) cc_final: 0.8598 (ttpp) REVERT: M 142 GLN cc_start: 0.8216 (tt0) cc_final: 0.7722 (tt0) REVERT: M 145 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8410 (mp0) REVERT: M 245 LYS cc_start: 0.8404 (pttm) cc_final: 0.8185 (mtpp) REVERT: M 373 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8144 (mtpt) REVERT: M 384 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7855 (mmtt) REVERT: M 397 GLN cc_start: 0.8479 (tt0) cc_final: 0.8228 (tt0) REVERT: M 402 MET cc_start: 0.8480 (mmt) cc_final: 0.8173 (mmm) REVERT: N 76 GLN cc_start: 0.8266 (mt0) cc_final: 0.7922 (mm-40) REVERT: N 221 LYS cc_start: 0.7194 (mmtp) cc_final: 0.6769 (mtmt) REVERT: N 266 ARG cc_start: 0.8958 (ttm170) cc_final: 0.8747 (ttm170) REVERT: N 302 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8288 (mm-30) REVERT: N 376 MET cc_start: 0.6899 (mmm) cc_final: 0.6642 (mmt) REVERT: O 125 LYS cc_start: 0.7172 (tttp) cc_final: 0.6948 (tmtt) REVERT: O 179 LYS cc_start: 0.6860 (mtmt) cc_final: 0.6301 (tptt) outliers start: 86 outliers final: 42 residues processed: 565 average time/residue: 0.2052 time to fit residues: 182.0574 Evaluate side-chains 479 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 427 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain M residue 73 GLN Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 361 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 258 optimal weight: 0.0670 chunk 219 optimal weight: 8.9990 chunk 347 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 349 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN F 94 HIS F 104 HIS ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 ASN I 335 ASN J 104 HIS M 155 ASN N 104 HIS N 331 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.166195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116875 restraints weight = 36232.881| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.87 r_work: 0.3092 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32649 Z= 0.102 Angle : 0.532 8.713 44497 Z= 0.282 Chirality : 0.044 0.169 4975 Planarity : 0.004 0.042 5721 Dihedral : 5.858 60.803 4507 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.40 % Allowed : 9.61 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.13), residues: 4110 helix: 1.94 (0.23), residues: 452 sheet: 0.13 (0.15), residues: 1204 loop : -0.26 (0.13), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 251 TYR 0.020 0.001 TYR F 199 PHE 0.011 0.001 PHE F 115 TRP 0.015 0.001 TRP K 268 HIS 0.009 0.001 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (32600) covalent geometry : angle 0.52974 / 0.28 (44399) SS BOND : bond 0.00456 / 0.27 ( 49) SS BOND : angle 1.06925 / 0.67 ( 98) hydrogen bonds : bond 0.03337 / 2.22 ( 1185) hydrogen bonds : angle 5.44670 / 3.84 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 479 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8741 (t) cc_final: 0.8377 (m) REVERT: A 97 ASP cc_start: 0.7667 (p0) cc_final: 0.7426 (m-30) REVERT: A 130 LYS cc_start: 0.8251 (ttpp) cc_final: 0.7725 (tttt) REVERT: A 160 LYS cc_start: 0.7897 (mttt) cc_final: 0.7688 (mttp) REVERT: A 183 ASP cc_start: 0.8219 (m-30) cc_final: 0.7978 (m-30) REVERT: A 347 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8124 (mttp) REVERT: A 366 LYS cc_start: 0.7920 (ptmt) cc_final: 0.7105 (pttt) REVERT: A 396 ASN cc_start: 0.8802 (t0) cc_final: 0.8582 (t0) REVERT: A 397 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: A 402 MET cc_start: 0.7814 (mmt) cc_final: 0.7341 (mmt) REVERT: B 13 ARG cc_start: 0.8112 (mtm180) cc_final: 0.7730 (ptp-170) REVERT: B 36 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7901 (ttpp) REVERT: B 58 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7984 (mtmt) REVERT: B 61 THR cc_start: 0.8395 (m) cc_final: 0.8084 (t) REVERT: B 70 MET cc_start: 0.8567 (mmm) cc_final: 0.8045 (mmm) REVERT: B 76 GLN cc_start: 0.8046 (mt0) cc_final: 0.7649 (mm-40) REVERT: B 84 ARG cc_start: 0.8659 (mtt90) cc_final: 0.8441 (mmt-90) REVERT: B 97 MET cc_start: 0.9302 (ttm) cc_final: 0.9065 (ttm) REVERT: B 120 SER cc_start: 0.7906 (m) cc_final: 0.7553 (t) REVERT: B 178 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7393 (mmt180) REVERT: B 199 TYR cc_start: 0.7999 (p90) cc_final: 0.7600 (p90) REVERT: B 214 ASP cc_start: 0.6447 (m-30) cc_final: 0.5457 (t0) REVERT: B 215 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7967 (ttpt) REVERT: B 222 ILE cc_start: 0.7968 (mm) cc_final: 0.7661 (mm) REVERT: B 265 CYS cc_start: 0.8218 (t) cc_final: 0.7857 (m) REVERT: B 285 ARG cc_start: 0.7757 (mtt180) cc_final: 0.6643 (mmm160) REVERT: B 315 GLU cc_start: 0.8671 (tt0) cc_final: 0.8396 (tt0) REVERT: B 322 GLU cc_start: 0.8059 (tp30) cc_final: 0.7790 (pt0) REVERT: C 112 MET cc_start: 0.5557 (pmt) cc_final: 0.4016 (tmm) REVERT: C 114 MET cc_start: 0.6714 (mpt) cc_final: 0.6079 (mpt) REVERT: C 162 LYS cc_start: 0.6710 (mtpt) cc_final: 0.6299 (tttp) REVERT: E 79 LYS cc_start: 0.8290 (mttt) cc_final: 0.7592 (tptm) REVERT: E 115 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8565 (mtmm) REVERT: E 145 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8080 (mp0) REVERT: E 249 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8746 (t) REVERT: E 341 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: E 345 LYS cc_start: 0.8554 (mttt) cc_final: 0.8292 (mmmt) REVERT: E 366 LYS cc_start: 0.8769 (mtpt) cc_final: 0.7695 (ttpp) REVERT: E 401 ASP cc_start: 0.7957 (t70) cc_final: 0.7558 (t0) REVERT: E 402 MET cc_start: 0.8042 (mmt) cc_final: 0.7764 (mmt) REVERT: F 4 GLU cc_start: 0.7840 (pt0) cc_final: 0.7233 (pm20) REVERT: F 36 LYS cc_start: 0.8608 (tttp) cc_final: 0.8102 (ttmt) REVERT: F 70 MET cc_start: 0.8800 (mmm) cc_final: 0.8553 (mmt) REVERT: F 120 SER cc_start: 0.7899 (m) cc_final: 0.7417 (p) REVERT: F 218 ASN cc_start: 0.7667 (m110) cc_final: 0.7465 (m110) REVERT: F 250 ARG cc_start: 0.8478 (ptt90) cc_final: 0.8176 (ptt180) REVERT: F 290 HIS cc_start: 0.9183 (OUTLIER) cc_final: 0.8613 (p-80) REVERT: F 353 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7219 (mt-10) REVERT: F 361 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6514 (pp) REVERT: G 114 MET cc_start: 0.6531 (ptp) cc_final: 0.6323 (ptp) REVERT: I 7 ILE cc_start: 0.7872 (pt) cc_final: 0.7532 (pt) REVERT: I 79 LYS cc_start: 0.8035 (mttt) cc_final: 0.7448 (mmmt) REVERT: I 147 PHE cc_start: 0.8121 (m-80) cc_final: 0.7807 (m-10) REVERT: I 373 LYS cc_start: 0.8426 (mttm) cc_final: 0.8087 (mtpt) REVERT: J 4 GLU cc_start: 0.8477 (tt0) cc_final: 0.7667 (tp30) REVERT: J 28 CYS cc_start: 0.8055 (t) cc_final: 0.7231 (p) REVERT: J 70 MET cc_start: 0.8564 (mmm) cc_final: 0.8128 (mmm) REVERT: J 79 LYS cc_start: 0.8451 (mttt) cc_final: 0.8032 (mtmm) REVERT: J 169 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.7376 (mpt) REVERT: J 298 SER cc_start: 0.9173 (t) cc_final: 0.8839 (m) REVERT: J 323 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8145 (mt-10) REVERT: J 376 MET cc_start: 0.7427 (mmm) cc_final: 0.7067 (ttp) REVERT: J 393 ARG cc_start: 0.5076 (ttp-170) cc_final: 0.4726 (mtp-110) REVERT: K 114 MET cc_start: 0.6301 (mpt) cc_final: 0.6087 (ptt) REVERT: K 163 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6522 (pttp) REVERT: M 65 THR cc_start: 0.8900 (t) cc_final: 0.8546 (p) REVERT: M 75 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8866 (t0) REVERT: M 79 LYS cc_start: 0.8498 (mttt) cc_final: 0.7746 (mmmt) REVERT: M 115 LYS cc_start: 0.8948 (tttt) cc_final: 0.8605 (ttpp) REVERT: M 130 LYS cc_start: 0.8504 (ttpp) cc_final: 0.7884 (tttm) REVERT: M 142 GLN cc_start: 0.8036 (tt0) cc_final: 0.7701 (tt0) REVERT: M 245 LYS cc_start: 0.8455 (pttm) cc_final: 0.8245 (mtpp) REVERT: M 373 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8221 (mtpt) REVERT: M 384 LYS cc_start: 0.8322 (mmtm) cc_final: 0.7904 (mmtt) REVERT: M 397 GLN cc_start: 0.8443 (tt0) cc_final: 0.8176 (tt0) REVERT: M 402 MET cc_start: 0.8568 (mmt) cc_final: 0.8248 (mmm) REVERT: N 76 GLN cc_start: 0.8269 (mt0) cc_final: 0.7889 (mm110) REVERT: N 200 ASN cc_start: 0.5703 (t0) cc_final: 0.5182 (t0) REVERT: N 302 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8387 (tp30) REVERT: N 325 ILE cc_start: 0.9243 (pp) cc_final: 0.9035 (pt) REVERT: N 376 MET cc_start: 0.6946 (mmm) cc_final: 0.6643 (mmt) REVERT: O 179 LYS cc_start: 0.6717 (mtmt) cc_final: 0.6182 (tptt) outliers start: 84 outliers final: 46 residues processed: 535 average time/residue: 0.2027 time to fit residues: 171.8969 Evaluate side-chains 482 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 427 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain M residue 73 GLN Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain O residue 147 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 33 optimal weight: 2.9990 chunk 382 optimal weight: 6.9990 chunk 386 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 400 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 HIS A 333 HIS B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN E 18 HIS E 411 GLN F 146 HIS F 247 GLN I 18 HIS I 102 GLN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 226 HIS J 287 HIS J 331 ASN M 18 HIS ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.158981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109233 restraints weight = 36214.406| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.84 r_work: 0.2995 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 32649 Z= 0.317 Angle : 0.677 11.046 44497 Z= 0.356 Chirality : 0.051 0.231 4975 Planarity : 0.005 0.049 5721 Dihedral : 5.930 59.898 4498 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 3.49 % Allowed : 10.38 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 4110 helix: 1.82 (0.23), residues: 451 sheet: -0.14 (0.14), residues: 1224 loop : -0.48 (0.13), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 178 TYR 0.024 0.003 TYR M 122 PHE 0.019 0.003 PHE M 240 TRP 0.013 0.002 TRP K 268 HIS 0.019 0.002 HIS J 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.32 (32600) covalent geometry : angle 0.67389 / 0.36 (44399) SS BOND : bond 0.00653 / 0.37 ( 49) SS BOND : angle 1.45497 / 0.98 ( 98) hydrogen bonds : bond 0.03686 / 2.46 ( 1185) hydrogen bonds : angle 5.61089 / 3.93 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 427 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8850 (t) cc_final: 0.8559 (m) REVERT: A 32 GLU cc_start: 0.8446 (tt0) cc_final: 0.8065 (tt0) REVERT: A 130 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7763 (tttt) REVERT: A 160 LYS cc_start: 0.7927 (mttt) cc_final: 0.7620 (mttp) REVERT: A 347 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8082 (mttp) REVERT: A 366 LYS cc_start: 0.8001 (ptmt) cc_final: 0.7792 (ptpp) REVERT: A 396 ASN cc_start: 0.8927 (t0) cc_final: 0.8701 (t0) REVERT: A 397 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: B 13 ARG cc_start: 0.8095 (mtm180) cc_final: 0.7658 (ptp-170) REVERT: B 61 THR cc_start: 0.8462 (m) cc_final: 0.8130 (t) REVERT: B 84 ARG cc_start: 0.8713 (mtt90) cc_final: 0.8509 (mmt-90) REVERT: B 117 ASP cc_start: 0.7398 (t0) cc_final: 0.7173 (t0) REVERT: B 120 SER cc_start: 0.8068 (m) cc_final: 0.7666 (t) REVERT: B 203 CYS cc_start: 0.4042 (OUTLIER) cc_final: 0.3607 (p) REVERT: B 214 ASP cc_start: 0.6440 (m-30) cc_final: 0.5591 (t0) REVERT: B 215 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7978 (ttpt) REVERT: B 265 CYS cc_start: 0.8532 (t) cc_final: 0.7770 (m) REVERT: B 285 ARG cc_start: 0.7858 (mtt180) cc_final: 0.6810 (mmm160) REVERT: B 315 GLU cc_start: 0.8704 (tt0) cc_final: 0.8415 (tt0) REVERT: C 112 MET cc_start: 0.5598 (pmt) cc_final: 0.4063 (tmm) REVERT: C 162 LYS cc_start: 0.6758 (mtpt) cc_final: 0.6344 (tttp) REVERT: E 79 LYS cc_start: 0.8238 (mttt) cc_final: 0.7441 (tptm) REVERT: E 115 LYS cc_start: 0.8961 (mtmm) cc_final: 0.8659 (mtmm) REVERT: E 145 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8231 (mp0) REVERT: E 230 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8357 (p-80) REVERT: E 341 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: E 345 LYS cc_start: 0.8641 (mttt) cc_final: 0.8394 (mmmt) REVERT: E 366 LYS cc_start: 0.8787 (mtpt) cc_final: 0.7611 (ttpp) REVERT: E 401 ASP cc_start: 0.7962 (t70) cc_final: 0.7463 (t0) REVERT: E 402 MET cc_start: 0.8216 (mmt) cc_final: 0.7822 (mmt) REVERT: F 4 GLU cc_start: 0.7909 (pt0) cc_final: 0.7287 (pm20) REVERT: F 36 LYS cc_start: 0.8600 (tttp) cc_final: 0.8106 (ttmt) REVERT: F 120 SER cc_start: 0.8299 (m) cc_final: 0.7816 (p) REVERT: F 250 ARG cc_start: 0.8553 (ptt90) cc_final: 0.8238 (ptt180) REVERT: F 290 HIS cc_start: 0.9250 (OUTLIER) cc_final: 0.8671 (p-80) REVERT: F 353 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7082 (mt-10) REVERT: F 401 LEU cc_start: 0.6181 (mp) cc_final: 0.5963 (mt) REVERT: I 68 CYS cc_start: 0.8644 (p) cc_final: 0.7703 (t) REVERT: I 79 LYS cc_start: 0.7899 (mttt) cc_final: 0.7203 (mmmt) REVERT: I 147 PHE cc_start: 0.8170 (m-80) cc_final: 0.7790 (m-10) REVERT: I 366 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7214 (ttpt) REVERT: J 4 GLU cc_start: 0.8502 (tt0) cc_final: 0.7703 (tp30) REVERT: J 28 CYS cc_start: 0.8135 (t) cc_final: 0.7141 (p) REVERT: J 79 LYS cc_start: 0.8475 (mttt) cc_final: 0.8132 (mttp) REVERT: J 97 MET cc_start: 0.8884 (ttt) cc_final: 0.8491 (ttt) REVERT: J 169 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7415 (mpt) REVERT: J 298 SER cc_start: 0.9096 (t) cc_final: 0.8743 (m) REVERT: J 376 MET cc_start: 0.7486 (mmm) cc_final: 0.7047 (ttt) REVERT: J 390 THR cc_start: 0.7314 (m) cc_final: 0.7050 (m) REVERT: J 393 ARG cc_start: 0.5177 (ttp-170) cc_final: 0.4819 (mtp-110) REVERT: K 114 MET cc_start: 0.6278 (mpt) cc_final: 0.6049 (ptt) REVERT: K 163 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6439 (pttp) REVERT: M 75 ASP cc_start: 0.9412 (OUTLIER) cc_final: 0.9021 (t0) REVERT: M 79 LYS cc_start: 0.8529 (mttt) cc_final: 0.7683 (mmmt) REVERT: M 115 LYS cc_start: 0.8948 (tttt) cc_final: 0.8626 (ttpp) REVERT: M 133 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8904 (mm) REVERT: M 142 GLN cc_start: 0.8264 (tt0) cc_final: 0.7701 (tt0) REVERT: M 373 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8331 (mtpt) REVERT: M 384 LYS cc_start: 0.8359 (mmtm) cc_final: 0.7902 (mmtt) REVERT: M 397 GLN cc_start: 0.8571 (tt0) cc_final: 0.8302 (tt0) REVERT: M 402 MET cc_start: 0.8692 (mmt) cc_final: 0.8367 (mmm) REVERT: N 76 GLN cc_start: 0.8351 (mt0) cc_final: 0.7858 (mm110) REVERT: N 246 ASP cc_start: 0.7948 (p0) cc_final: 0.7748 (p0) REVERT: N 366 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8080 (m) REVERT: O 179 LYS cc_start: 0.6488 (mtmt) cc_final: 0.5932 (tptt) outliers start: 122 outliers final: 79 residues processed: 516 average time/residue: 0.2122 time to fit residues: 174.8821 Evaluate side-chains 500 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 410 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 276 THR Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 235 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 286 optimal weight: 7.9990 chunk 305 optimal weight: 0.9980 chunk 387 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 358 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN I 30 GLN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 128 GLN J 236 GLN ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109601 restraints weight = 36375.082| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.82 r_work: 0.2986 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32649 Z= 0.220 Angle : 0.599 10.257 44497 Z= 0.316 Chirality : 0.047 0.192 4975 Planarity : 0.005 0.048 5721 Dihedral : 5.751 58.476 4498 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 3.35 % Allowed : 11.56 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 4110 helix: 1.96 (0.23), residues: 452 sheet: -0.28 (0.14), residues: 1245 loop : -0.49 (0.13), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 251 TYR 0.023 0.002 TYR F 199 PHE 0.014 0.002 PHE B 100 TRP 0.012 0.001 TRP K 268 HIS 0.010 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.22 (32600) covalent geometry : angle 0.59675 / 0.31 (44399) SS BOND : bond 0.00561 / 0.30 ( 49) SS BOND : angle 1.33124 / 0.88 ( 98) hydrogen bonds : bond 0.03388 / 2.25 ( 1185) hydrogen bonds : angle 5.43744 / 3.80 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 427 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8833 (t) cc_final: 0.8556 (m) REVERT: A 32 GLU cc_start: 0.8379 (tt0) cc_final: 0.7940 (tt0) REVERT: A 130 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7681 (tttt) REVERT: A 160 LYS cc_start: 0.7854 (mttt) cc_final: 0.7549 (mttp) REVERT: A 347 LYS cc_start: 0.8314 (mmtt) cc_final: 0.8065 (mttp) REVERT: A 366 LYS cc_start: 0.7936 (ptmt) cc_final: 0.7036 (pttt) REVERT: A 396 ASN cc_start: 0.9002 (t0) cc_final: 0.8763 (t0) REVERT: A 397 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: B 13 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7687 (ptp-170) REVERT: B 61 THR cc_start: 0.8388 (m) cc_final: 0.8084 (t) REVERT: B 120 SER cc_start: 0.7958 (m) cc_final: 0.7579 (t) REVERT: B 203 CYS cc_start: 0.4376 (OUTLIER) cc_final: 0.4073 (p) REVERT: B 214 ASP cc_start: 0.6238 (m-30) cc_final: 0.5408 (t0) REVERT: B 215 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7961 (ttpt) REVERT: B 265 CYS cc_start: 0.8383 (t) cc_final: 0.7809 (m) REVERT: B 285 ARG cc_start: 0.7788 (mtt180) cc_final: 0.6687 (mmm160) REVERT: B 315 GLU cc_start: 0.8672 (tt0) cc_final: 0.8347 (tt0) REVERT: C 112 MET cc_start: 0.5530 (pmt) cc_final: 0.4115 (tmm) REVERT: C 162 LYS cc_start: 0.6680 (mtpt) cc_final: 0.6285 (tttp) REVERT: E 79 LYS cc_start: 0.8118 (mttt) cc_final: 0.7306 (tptm) REVERT: E 115 LYS cc_start: 0.8999 (mtmm) cc_final: 0.8565 (mtmm) REVERT: E 145 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8215 (mp0) REVERT: E 230 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.8302 (p-80) REVERT: E 321 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7620 (ptpp) REVERT: E 345 LYS cc_start: 0.8645 (mttt) cc_final: 0.8354 (mmmt) REVERT: E 366 LYS cc_start: 0.8744 (mtpt) cc_final: 0.7520 (ttpp) REVERT: E 401 ASP cc_start: 0.7974 (t70) cc_final: 0.7464 (t0) REVERT: E 402 MET cc_start: 0.8141 (mmt) cc_final: 0.7770 (mmt) REVERT: F 4 GLU cc_start: 0.7899 (pt0) cc_final: 0.7257 (pm20) REVERT: F 36 LYS cc_start: 0.8544 (tttp) cc_final: 0.8047 (ttmt) REVERT: F 120 SER cc_start: 0.8365 (m) cc_final: 0.7858 (p) REVERT: F 250 ARG cc_start: 0.8558 (ptt90) cc_final: 0.8231 (ptt180) REVERT: F 290 HIS cc_start: 0.9223 (OUTLIER) cc_final: 0.8646 (p-80) REVERT: F 353 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6966 (mt-10) REVERT: F 361 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6615 (pp) REVERT: G 216 LYS cc_start: 0.8154 (tptt) cc_final: 0.7703 (mmtm) REVERT: I 68 CYS cc_start: 0.8499 (p) cc_final: 0.8055 (t) REVERT: I 79 LYS cc_start: 0.7856 (mttt) cc_final: 0.7109 (mmmt) REVERT: I 147 PHE cc_start: 0.8149 (m-80) cc_final: 0.7776 (m-10) REVERT: I 366 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7147 (ttpt) REVERT: J 4 GLU cc_start: 0.8513 (tt0) cc_final: 0.7770 (tp30) REVERT: J 28 CYS cc_start: 0.7949 (t) cc_final: 0.7051 (p) REVERT: J 51 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8815 (m) REVERT: J 79 LYS cc_start: 0.8496 (mttt) cc_final: 0.8075 (mttp) REVERT: J 80 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7772 (tmt170) REVERT: J 169 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7338 (mpt) REVERT: J 298 SER cc_start: 0.9056 (t) cc_final: 0.8717 (m) REVERT: J 376 MET cc_start: 0.7432 (mmm) cc_final: 0.7092 (ttp) REVERT: J 390 THR cc_start: 0.7220 (m) cc_final: 0.6964 (m) REVERT: J 393 ARG cc_start: 0.5120 (ttp-170) cc_final: 0.4772 (mtp-110) REVERT: K 114 MET cc_start: 0.6289 (mpt) cc_final: 0.6059 (ptt) REVERT: K 163 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6534 (ptmm) REVERT: M 75 ASP cc_start: 0.9358 (OUTLIER) cc_final: 0.9016 (t0) REVERT: M 79 LYS cc_start: 0.8438 (mttt) cc_final: 0.7712 (mttp) REVERT: M 115 LYS cc_start: 0.8906 (tttt) cc_final: 0.8623 (ttpp) REVERT: M 130 LYS cc_start: 0.8532 (ttpp) cc_final: 0.7832 (tttm) REVERT: M 133 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8825 (mm) REVERT: M 142 GLN cc_start: 0.8256 (tt0) cc_final: 0.7667 (tt0) REVERT: M 373 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8258 (mtpt) REVERT: M 384 LYS cc_start: 0.8350 (mmtm) cc_final: 0.7868 (mmtt) REVERT: M 397 GLN cc_start: 0.8575 (tt0) cc_final: 0.8301 (tt0) REVERT: M 402 MET cc_start: 0.8655 (mmt) cc_final: 0.8324 (mmm) REVERT: N 76 GLN cc_start: 0.8308 (mt0) cc_final: 0.7785 (mm110) REVERT: N 344 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: N 366 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.8024 (m) REVERT: O 179 LYS cc_start: 0.6430 (mtmt) cc_final: 0.5966 (tptt) outliers start: 117 outliers final: 77 residues processed: 508 average time/residue: 0.2081 time to fit residues: 168.7355 Evaluate side-chains 500 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 409 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain M residue 73 GLN Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 212 ASP Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 64 HIS Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 344 GLU Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain Z residue 139 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 289 optimal weight: 9.9990 chunk 396 optimal weight: 7.9990 chunk 356 optimal weight: 0.5980 chunk 195 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 346 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 ASN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 64 HIS J 236 GLN ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110065 restraints weight = 36375.802| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.89 r_work: 0.2972 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 32649 Z= 0.240 Angle : 0.608 10.174 44497 Z= 0.320 Chirality : 0.048 0.202 4975 Planarity : 0.005 0.051 5721 Dihedral : 5.594 58.190 4492 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.38 % Favored : 95.60 % Rotamer: Outliers : 3.72 % Allowed : 11.99 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 4110 helix: 1.97 (0.24), residues: 452 sheet: -0.35 (0.14), residues: 1237 loop : -0.54 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 251 TYR 0.022 0.002 TYR A 137 PHE 0.015 0.002 PHE M 163 TRP 0.012 0.001 TRP K 268 HIS 0.010 0.001 HIS I 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.24 (32600) covalent geometry : angle 0.60608 / 0.32 (44399) SS BOND : bond 0.00590 / 0.33 ( 49) SS BOND : angle 1.30213 / 0.90 ( 98) hydrogen bonds : bond 0.03398 / 2.26 ( 1185) hydrogen bonds : angle 5.41889 / 3.79 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 405 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8870 (t) cc_final: 0.8600 (m) REVERT: A 32 GLU cc_start: 0.8491 (tt0) cc_final: 0.8052 (tt0) REVERT: A 130 LYS cc_start: 0.8321 (ttpp) cc_final: 0.7757 (tttt) REVERT: A 160 LYS cc_start: 0.7920 (mttt) cc_final: 0.7616 (mttp) REVERT: A 347 LYS cc_start: 0.8354 (mmtt) cc_final: 0.8097 (mttp) REVERT: A 366 LYS cc_start: 0.7986 (ptmt) cc_final: 0.7064 (pttt) REVERT: A 396 ASN cc_start: 0.9080 (t0) cc_final: 0.8669 (t0) REVERT: A 397 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: B 13 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7751 (ptp-170) REVERT: B 36 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7868 (ttpp) REVERT: B 61 THR cc_start: 0.8443 (m) cc_final: 0.8149 (t) REVERT: B 120 SER cc_start: 0.8032 (m) cc_final: 0.7646 (t) REVERT: B 203 CYS cc_start: 0.4584 (OUTLIER) cc_final: 0.4307 (p) REVERT: B 214 ASP cc_start: 0.6267 (m-30) cc_final: 0.5448 (t0) REVERT: B 215 LYS cc_start: 0.8334 (ttpt) cc_final: 0.7943 (tttt) REVERT: B 265 CYS cc_start: 0.8537 (t) cc_final: 0.7742 (m) REVERT: B 285 ARG cc_start: 0.7839 (mtt180) cc_final: 0.6752 (mmm160) REVERT: B 315 GLU cc_start: 0.8682 (tt0) cc_final: 0.8389 (tt0) REVERT: B 322 GLU cc_start: 0.8523 (pt0) cc_final: 0.8029 (tp30) REVERT: C 112 MET cc_start: 0.5508 (pmt) cc_final: 0.4285 (tmm) REVERT: C 162 LYS cc_start: 0.6757 (mtpt) cc_final: 0.6326 (tttp) REVERT: E 79 LYS cc_start: 0.8212 (mttt) cc_final: 0.7367 (tptm) REVERT: E 115 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8651 (mtmm) REVERT: E 145 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8272 (mp0) REVERT: E 230 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8375 (p-80) REVERT: E 321 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7565 (ptpp) REVERT: E 345 LYS cc_start: 0.8676 (mttt) cc_final: 0.8372 (mmmt) REVERT: E 366 LYS cc_start: 0.8774 (mtpt) cc_final: 0.7693 (ttpp) REVERT: E 401 ASP cc_start: 0.8005 (t70) cc_final: 0.7489 (t0) REVERT: E 402 MET cc_start: 0.8102 (mmt) cc_final: 0.7804 (mmt) REVERT: F 36 LYS cc_start: 0.8597 (tttp) cc_final: 0.8115 (ttmt) REVERT: F 120 SER cc_start: 0.8401 (m) cc_final: 0.7949 (p) REVERT: F 290 HIS cc_start: 0.9254 (OUTLIER) cc_final: 0.8678 (p-80) REVERT: F 353 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7015 (mt-10) REVERT: F 361 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6699 (pp) REVERT: G 216 LYS cc_start: 0.8189 (tptt) cc_final: 0.7772 (tptp) REVERT: I 79 LYS cc_start: 0.7802 (mttt) cc_final: 0.7016 (mmmt) REVERT: I 147 PHE cc_start: 0.8191 (m-80) cc_final: 0.7810 (m-10) REVERT: I 366 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7379 (ttpt) REVERT: J 28 CYS cc_start: 0.8000 (t) cc_final: 0.7121 (p) REVERT: J 79 LYS cc_start: 0.8524 (mttt) cc_final: 0.8111 (mttp) REVERT: J 80 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7802 (tmt170) REVERT: J 97 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8589 (ttp) REVERT: J 169 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7383 (mpt) REVERT: J 298 SER cc_start: 0.9080 (t) cc_final: 0.8750 (m) REVERT: J 376 MET cc_start: 0.7455 (mmm) cc_final: 0.7027 (ttt) REVERT: J 390 THR cc_start: 0.7257 (m) cc_final: 0.7003 (m) REVERT: J 393 ARG cc_start: 0.5244 (ttp-170) cc_final: 0.4872 (mtp-110) REVERT: K 114 MET cc_start: 0.6303 (mpt) cc_final: 0.6063 (ptt) REVERT: K 163 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6615 (ptmm) REVERT: M 75 ASP cc_start: 0.9366 (OUTLIER) cc_final: 0.9032 (t0) REVERT: M 79 LYS cc_start: 0.8439 (mttt) cc_final: 0.7743 (mttp) REVERT: M 115 LYS cc_start: 0.8934 (tttt) cc_final: 0.8661 (ttpp) REVERT: M 129 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8751 (tt) REVERT: M 130 LYS cc_start: 0.8608 (ttpp) cc_final: 0.7967 (tttm) REVERT: M 133 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8886 (mm) REVERT: M 135 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8534 (mm) REVERT: M 142 GLN cc_start: 0.8321 (tt0) cc_final: 0.7745 (tt0) REVERT: M 300 SER cc_start: 0.8857 (p) cc_final: 0.8601 (p) REVERT: M 320 TYR cc_start: 0.8845 (p90) cc_final: 0.8598 (p90) REVERT: M 373 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8321 (mtpt) REVERT: M 384 LYS cc_start: 0.8373 (mmtm) cc_final: 0.7846 (mmtt) REVERT: M 397 GLN cc_start: 0.8604 (tt0) cc_final: 0.8342 (tt0) REVERT: M 402 MET cc_start: 0.8688 (mmt) cc_final: 0.8346 (mmm) REVERT: N 344 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: N 366 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8122 (m) REVERT: O 179 LYS cc_start: 0.6486 (mtmt) cc_final: 0.5928 (tptt) outliers start: 130 outliers final: 90 residues processed: 493 average time/residue: 0.2089 time to fit residues: 164.2724 Evaluate side-chains 495 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 388 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 203 CYS Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 212 ASP Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 64 HIS Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 344 GLU Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain O residue 210 ILE Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain Z residue 139 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 298 optimal weight: 0.8980 chunk 380 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 201 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 385 optimal weight: 8.9990 chunk 388 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN C 195 ASN E 264 ASN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 94 HIS J 236 GLN ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.161322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112177 restraints weight = 36445.215| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.86 r_work: 0.3034 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32649 Z= 0.161 Angle : 0.556 9.496 44497 Z= 0.292 Chirality : 0.045 0.183 4975 Planarity : 0.004 0.050 5721 Dihedral : 5.400 59.128 4492 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 3.09 % Allowed : 12.70 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4110 helix: 2.17 (0.24), residues: 452 sheet: -0.33 (0.14), residues: 1256 loop : -0.47 (0.13), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 251 TYR 0.024 0.002 TYR A 137 PHE 0.015 0.001 PHE A 312 TRP 0.012 0.001 TRP K 268 HIS 0.008 0.001 HIS M 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (32600) covalent geometry : angle 0.55291 / 0.29 (44399) SS BOND : bond 0.00450 / 0.25 ( 49) SS BOND : angle 1.40266 / 0.89 ( 98) hydrogen bonds : bond 0.03135 / 2.09 ( 1185) hydrogen bonds : angle 5.25836 / 3.68 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 422 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8842 (t) cc_final: 0.8575 (m) REVERT: A 32 GLU cc_start: 0.8447 (tt0) cc_final: 0.7991 (tt0) REVERT: A 130 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7675 (tttt) REVERT: A 160 LYS cc_start: 0.7812 (mttt) cc_final: 0.7585 (mttp) REVERT: A 347 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8138 (mttp) REVERT: A 351 LYS cc_start: 0.8415 (ptpp) cc_final: 0.8114 (mtpp) REVERT: A 366 LYS cc_start: 0.7911 (ptmt) cc_final: 0.7443 (ptpp) REVERT: A 396 ASN cc_start: 0.9028 (t0) cc_final: 0.8736 (t0) REVERT: A 397 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: B 13 ARG cc_start: 0.8141 (mtm180) cc_final: 0.7803 (ptp-170) REVERT: B 36 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7860 (ttpp) REVERT: B 61 THR cc_start: 0.8414 (m) cc_final: 0.8138 (t) REVERT: B 76 GLN cc_start: 0.8111 (mt0) cc_final: 0.7600 (mm-40) REVERT: B 120 SER cc_start: 0.7975 (m) cc_final: 0.7600 (t) REVERT: B 203 CYS cc_start: 0.4587 (OUTLIER) cc_final: 0.4297 (p) REVERT: B 214 ASP cc_start: 0.6114 (m-30) cc_final: 0.5209 (t0) REVERT: B 215 LYS cc_start: 0.8332 (ttpt) cc_final: 0.7997 (tttt) REVERT: B 265 CYS cc_start: 0.8375 (t) cc_final: 0.7760 (m) REVERT: B 285 ARG cc_start: 0.7772 (mtt180) cc_final: 0.6678 (mmm160) REVERT: B 315 GLU cc_start: 0.8645 (tt0) cc_final: 0.8330 (tt0) REVERT: C 112 MET cc_start: 0.5642 (pmt) cc_final: 0.4573 (tmm) REVERT: C 162 LYS cc_start: 0.6674 (mtpt) cc_final: 0.6246 (tttp) REVERT: E 66 SER cc_start: 0.8411 (t) cc_final: 0.8030 (p) REVERT: E 79 LYS cc_start: 0.8177 (mttt) cc_final: 0.7283 (tptm) REVERT: E 115 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8617 (mtmm) REVERT: E 133 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8611 (mm) REVERT: E 145 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8199 (mp0) REVERT: E 230 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8152 (p-80) REVERT: E 297 THR cc_start: 0.8654 (p) cc_final: 0.8191 (p) REVERT: E 321 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7663 (ptpp) REVERT: E 345 LYS cc_start: 0.8655 (mttt) cc_final: 0.8352 (mmmt) REVERT: E 366 LYS cc_start: 0.8732 (mtpt) cc_final: 0.7651 (ttpp) REVERT: E 397 GLN cc_start: 0.8464 (tt0) cc_final: 0.8170 (tt0) REVERT: E 401 ASP cc_start: 0.7949 (t70) cc_final: 0.7472 (t0) REVERT: E 411 GLN cc_start: 0.6885 (mt0) cc_final: 0.6584 (mt0) REVERT: F 36 LYS cc_start: 0.8533 (tttp) cc_final: 0.8063 (ttmt) REVERT: F 109 ASP cc_start: 0.8636 (p0) cc_final: 0.8426 (p0) REVERT: F 120 SER cc_start: 0.8434 (m) cc_final: 0.7961 (p) REVERT: F 290 HIS cc_start: 0.9224 (OUTLIER) cc_final: 0.8620 (p-80) REVERT: F 353 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6947 (mt-10) REVERT: F 361 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6354 (pp) REVERT: F 397 THR cc_start: 0.6250 (OUTLIER) cc_final: 0.5937 (m) REVERT: G 114 MET cc_start: 0.6378 (ptp) cc_final: 0.6162 (ptp) REVERT: I 79 LYS cc_start: 0.7804 (mttt) cc_final: 0.6752 (tptp) REVERT: I 147 PHE cc_start: 0.8190 (m-80) cc_final: 0.7830 (m-10) REVERT: I 366 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7229 (ttpt) REVERT: J 13 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7255 (ttt180) REVERT: J 28 CYS cc_start: 0.7953 (t) cc_final: 0.7056 (p) REVERT: J 32 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8198 (p) REVERT: J 79 LYS cc_start: 0.8466 (mttt) cc_final: 0.8019 (mttp) REVERT: J 97 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8615 (ttp) REVERT: J 169 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7312 (mpt) REVERT: J 250 ARG cc_start: 0.8572 (ptt90) cc_final: 0.7895 (ptt-90) REVERT: J 298 SER cc_start: 0.9050 (t) cc_final: 0.8727 (m) REVERT: J 376 MET cc_start: 0.7399 (mmm) cc_final: 0.6973 (ttt) REVERT: J 390 THR cc_start: 0.7177 (m) cc_final: 0.6931 (m) REVERT: J 393 ARG cc_start: 0.5171 (ttp-170) cc_final: 0.4781 (mtp-110) REVERT: K 114 MET cc_start: 0.6301 (mpt) cc_final: 0.6065 (ptt) REVERT: K 163 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6699 (ptmm) REVERT: M 75 ASP cc_start: 0.9283 (OUTLIER) cc_final: 0.8956 (t0) REVERT: M 79 LYS cc_start: 0.8407 (mttt) cc_final: 0.7676 (mttp) REVERT: M 115 LYS cc_start: 0.8903 (tttt) cc_final: 0.8629 (ttpp) REVERT: M 130 LYS cc_start: 0.8499 (ttpp) cc_final: 0.7874 (tttm) REVERT: M 142 GLN cc_start: 0.8239 (tt0) cc_final: 0.7689 (tt0) REVERT: M 300 SER cc_start: 0.8840 (p) cc_final: 0.8571 (p) REVERT: M 373 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8263 (mtpt) REVERT: M 384 LYS cc_start: 0.8348 (mmtm) cc_final: 0.7817 (mmtt) REVERT: M 397 GLN cc_start: 0.8553 (tt0) cc_final: 0.8287 (tt0) REVERT: M 402 MET cc_start: 0.8602 (mmt) cc_final: 0.8264 (mmm) REVERT: N 344 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: N 366 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8024 (m) REVERT: O 179 LYS cc_start: 0.6509 (mtmt) cc_final: 0.5948 (tptt) outliers start: 108 outliers final: 75 residues processed: 496 average time/residue: 0.2023 time to fit residues: 161.8674 Evaluate side-chains 494 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 403 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain M residue 73 GLN Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 212 ASP Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 302 GLN Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 344 GLU Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 210 ILE Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain Z residue 139 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 220 optimal weight: 0.0770 chunk 37 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 93 optimal weight: 30.0000 chunk 365 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 353 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 ASN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 94 HIS J 232 HIS J 236 GLN ** K 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.156821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115240 restraints weight = 36493.507| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.06 r_work: 0.2932 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 32649 Z= 0.234 Angle : 0.605 12.125 44497 Z= 0.317 Chirality : 0.048 0.227 4975 Planarity : 0.005 0.054 5721 Dihedral : 5.491 58.577 4491 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.48 % Favored : 95.50 % Rotamer: Outliers : 3.60 % Allowed : 12.21 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 4110 helix: 2.14 (0.24), residues: 452 sheet: -0.38 (0.14), residues: 1252 loop : -0.56 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 251 TYR 0.025 0.002 TYR A 137 PHE 0.016 0.002 PHE I 13 TRP 0.011 0.001 TRP K 268 HIS 0.010 0.001 HIS I 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.23 (32600) covalent geometry : angle 0.60180 / 0.32 (44399) SS BOND : bond 0.00524 / 0.30 ( 49) SS BOND : angle 1.43087 / 0.93 ( 98) hydrogen bonds : bond 0.03310 / 2.20 ( 1185) hydrogen bonds : angle 5.33428 / 3.73 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 400 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8383 (tttt) REVERT: A 347 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8374 (mttp) REVERT: A 351 LYS cc_start: 0.8603 (ptpp) cc_final: 0.8312 (mtpp) REVERT: A 366 LYS cc_start: 0.8493 (ptmt) cc_final: 0.8026 (ptpp) REVERT: A 396 ASN cc_start: 0.9219 (t0) cc_final: 0.8935 (t0) REVERT: A 397 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: B 36 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8049 (ttpp) REVERT: B 120 SER cc_start: 0.8579 (m) cc_final: 0.8203 (t) REVERT: B 203 CYS cc_start: 0.4840 (OUTLIER) cc_final: 0.4589 (p) REVERT: B 214 ASP cc_start: 0.6813 (m-30) cc_final: 0.6045 (t0) REVERT: B 215 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8159 (tttt) REVERT: B 265 CYS cc_start: 0.8480 (t) cc_final: 0.8173 (m) REVERT: B 285 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7314 (mmm160) REVERT: C 112 MET cc_start: 0.5500 (pmt) cc_final: 0.4677 (tmm) REVERT: C 162 LYS cc_start: 0.7218 (mtpt) cc_final: 0.6808 (tttp) REVERT: E 66 SER cc_start: 0.8635 (t) cc_final: 0.8424 (p) REVERT: E 79 LYS cc_start: 0.8497 (mttt) cc_final: 0.8038 (tptm) REVERT: E 115 LYS cc_start: 0.9121 (mtmm) cc_final: 0.8731 (mtmm) REVERT: E 133 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8936 (mm) REVERT: E 145 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8392 (mp0) REVERT: E 297 THR cc_start: 0.8879 (p) cc_final: 0.8566 (p) REVERT: E 321 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7910 (ptpp) REVERT: E 366 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8308 (ttpp) REVERT: E 397 GLN cc_start: 0.8669 (tt0) cc_final: 0.8447 (tt0) REVERT: E 401 ASP cc_start: 0.8027 (t70) cc_final: 0.7810 (t0) REVERT: F 36 LYS cc_start: 0.8617 (tttp) cc_final: 0.8399 (ttmt) REVERT: F 120 SER cc_start: 0.8683 (m) cc_final: 0.8247 (p) REVERT: F 290 HIS cc_start: 0.9180 (OUTLIER) cc_final: 0.8656 (p-80) REVERT: F 353 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7906 (mt-10) REVERT: F 361 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7385 (pp) REVERT: F 397 THR cc_start: 0.6792 (OUTLIER) cc_final: 0.6476 (p) REVERT: G 142 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6909 (mpp) REVERT: G 158 LYS cc_start: 0.8102 (pttp) cc_final: 0.7890 (pttt) REVERT: G 216 LYS cc_start: 0.8092 (tptt) cc_final: 0.7702 (tptp) REVERT: I 79 LYS cc_start: 0.8235 (mttt) cc_final: 0.7865 (mtpp) REVERT: I 147 PHE cc_start: 0.8493 (m-80) cc_final: 0.8182 (m-10) REVERT: I 366 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8001 (ttpt) REVERT: J 13 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7803 (ttt180) REVERT: J 28 CYS cc_start: 0.8033 (t) cc_final: 0.7787 (p) REVERT: J 79 LYS cc_start: 0.8604 (mttt) cc_final: 0.8372 (mttp) REVERT: J 80 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8108 (tmt170) REVERT: J 97 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8515 (ttt) REVERT: J 169 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.7972 (mpt) REVERT: J 250 ARG cc_start: 0.8707 (ptt90) cc_final: 0.8262 (ptt-90) REVERT: J 298 SER cc_start: 0.9044 (t) cc_final: 0.8806 (m) REVERT: J 376 MET cc_start: 0.7809 (mmm) cc_final: 0.7499 (ttt) REVERT: J 390 THR cc_start: 0.7837 (m) cc_final: 0.7558 (m) REVERT: J 393 ARG cc_start: 0.5865 (ttp-170) cc_final: 0.5426 (mtp-110) REVERT: K 114 MET cc_start: 0.6394 (mpt) cc_final: 0.6150 (ptt) REVERT: K 163 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.6981 (ptmm) REVERT: M 75 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8882 (t0) REVERT: M 79 LYS cc_start: 0.8626 (mttt) cc_final: 0.8138 (mttp) REVERT: M 130 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8366 (tttm) REVERT: M 133 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9085 (mm) REVERT: M 142 GLN cc_start: 0.8478 (tt0) cc_final: 0.8026 (tt0) REVERT: M 384 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8001 (mmtt) REVERT: N 344 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: N 366 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8585 (m) REVERT: O 179 LYS cc_start: 0.6716 (mtmt) cc_final: 0.6023 (tptt) outliers start: 126 outliers final: 93 residues processed: 491 average time/residue: 0.2032 time to fit residues: 161.1784 Evaluate side-chains 494 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 384 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 203 CYS Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 212 ASP Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 280 MET Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 302 GLN Chi-restraints excluded: chain M residue 305 VAL Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 153 CYS Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 344 GLU Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 210 ILE Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain Z residue 139 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 266 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 360 optimal weight: 9.9990 chunk 324 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 349 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN E 264 ASN F 226 HIS ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 94 HIS K 177 HIS ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.158985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117860 restraints weight = 36458.750| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.15 r_work: 0.2971 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32649 Z= 0.129 Angle : 0.537 9.670 44497 Z= 0.282 Chirality : 0.045 0.196 4975 Planarity : 0.004 0.052 5721 Dihedral : 5.257 59.751 4491 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.33 % Rotamer: Outliers : 2.95 % Allowed : 12.99 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4110 helix: 2.14 (0.24), residues: 476 sheet: -0.37 (0.14), residues: 1261 loop : -0.54 (0.13), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 251 TYR 0.026 0.001 TYR A 137 PHE 0.015 0.001 PHE I 13 TRP 0.011 0.001 TRP K 268 HIS 0.007 0.001 HIS M 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (32600) covalent geometry : angle 0.53353 / 0.28 (44399) SS BOND : bond 0.00324 / 0.18 ( 49) SS BOND : angle 1.37666 / 0.90 ( 98) hydrogen bonds : bond 0.03012 / 2.00 ( 1185) hydrogen bonds : angle 5.14106 / 3.60 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 420 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8359 (tttt) REVERT: A 347 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8349 (mttp) REVERT: A 351 LYS cc_start: 0.8551 (ptpp) cc_final: 0.8308 (mtpp) REVERT: A 366 LYS cc_start: 0.8468 (ptmt) cc_final: 0.8008 (ptpp) REVERT: A 396 ASN cc_start: 0.9200 (t0) cc_final: 0.8893 (t0) REVERT: B 36 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8103 (ttpp) REVERT: B 76 GLN cc_start: 0.8448 (mt0) cc_final: 0.8192 (mm-40) REVERT: B 120 SER cc_start: 0.8666 (m) cc_final: 0.8330 (t) REVERT: B 203 CYS cc_start: 0.4697 (OUTLIER) cc_final: 0.4489 (p) REVERT: B 214 ASP cc_start: 0.6638 (m-30) cc_final: 0.5860 (t0) REVERT: B 215 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8204 (tttt) REVERT: B 285 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7269 (mmm160) REVERT: C 112 MET cc_start: 0.5394 (pmt) cc_final: 0.4651 (tmm) REVERT: C 142 MET cc_start: 0.7054 (mmm) cc_final: 0.6816 (mmm) REVERT: C 162 LYS cc_start: 0.7177 (mtpt) cc_final: 0.6803 (tttp) REVERT: E 79 LYS cc_start: 0.8460 (mttt) cc_final: 0.8027 (tptm) REVERT: E 115 LYS cc_start: 0.9080 (mtmm) cc_final: 0.8700 (mtmm) REVERT: E 145 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8403 (mp0) REVERT: E 297 THR cc_start: 0.8875 (p) cc_final: 0.8576 (p) REVERT: E 321 LYS cc_start: 0.8347 (mtmm) cc_final: 0.8003 (ptpp) REVERT: E 366 LYS cc_start: 0.9120 (mtpt) cc_final: 0.8333 (ttpp) REVERT: F 36 LYS cc_start: 0.8591 (tttp) cc_final: 0.8379 (ttmt) REVERT: F 120 SER cc_start: 0.8663 (m) cc_final: 0.8232 (p) REVERT: F 290 HIS cc_start: 0.9134 (OUTLIER) cc_final: 0.8577 (p-80) REVERT: F 353 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7889 (mt-10) REVERT: F 361 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7224 (pp) REVERT: G 142 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6848 (mpp) REVERT: G 216 LYS cc_start: 0.8073 (tptt) cc_final: 0.7653 (tptp) REVERT: I 79 LYS cc_start: 0.8233 (mttt) cc_final: 0.7868 (mtpp) REVERT: I 147 PHE cc_start: 0.8473 (m-80) cc_final: 0.8177 (m-10) REVERT: I 242 TYR cc_start: 0.8559 (m-10) cc_final: 0.8357 (m-80) REVERT: I 366 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7921 (ttpt) REVERT: J 13 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7825 (ttt180) REVERT: J 70 MET cc_start: 0.8709 (tpp) cc_final: 0.8437 (tpp) REVERT: J 79 LYS cc_start: 0.8518 (mttt) cc_final: 0.8249 (mtmm) REVERT: J 97 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8683 (ttp) REVERT: J 169 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.7904 (mpt) REVERT: J 250 ARG cc_start: 0.8696 (ptt90) cc_final: 0.8309 (ptt-90) REVERT: J 298 SER cc_start: 0.9015 (t) cc_final: 0.8800 (m) REVERT: J 376 MET cc_start: 0.7797 (mmm) cc_final: 0.7481 (ttt) REVERT: J 390 THR cc_start: 0.7835 (m) cc_final: 0.7562 (m) REVERT: J 393 ARG cc_start: 0.5838 (ttp-170) cc_final: 0.5418 (mtp-110) REVERT: K 114 MET cc_start: 0.6363 (mpt) cc_final: 0.6107 (ptt) REVERT: K 163 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7005 (ptmm) REVERT: M 75 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8853 (t0) REVERT: M 79 LYS cc_start: 0.8594 (mttt) cc_final: 0.8117 (mttp) REVERT: M 130 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8344 (tttm) REVERT: M 142 GLN cc_start: 0.8386 (tt0) cc_final: 0.7960 (tt0) REVERT: M 384 LYS cc_start: 0.8444 (mmtm) cc_final: 0.7988 (mmtt) REVERT: N 344 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7492 (mm-30) REVERT: N 366 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8533 (m) REVERT: O 179 LYS cc_start: 0.6683 (mtmt) cc_final: 0.5986 (tptt) outliers start: 103 outliers final: 79 residues processed: 491 average time/residue: 0.2000 time to fit residues: 159.4339 Evaluate side-chains 488 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 397 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain M residue 73 GLN Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 344 GLU Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 210 ILE Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain Z residue 139 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 ASN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 94 HIS J 236 GLN ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.158901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118397 restraints weight = 36502.736| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.25 r_work: 0.2953 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32649 Z= 0.156 Angle : 0.557 12.229 44497 Z= 0.291 Chirality : 0.046 0.220 4975 Planarity : 0.004 0.051 5721 Dihedral : 5.255 59.414 4491 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 2.83 % Allowed : 13.59 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4110 helix: 2.19 (0.24), residues: 476 sheet: -0.35 (0.14), residues: 1249 loop : -0.56 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 251 TYR 0.027 0.002 TYR A 137 PHE 0.016 0.001 PHE I 13 TRP 0.011 0.001 TRP K 268 HIS 0.008 0.001 HIS M 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (32600) covalent geometry : angle 0.55360 / 0.29 (44399) SS BOND : bond 0.00367 / 0.21 ( 49) SS BOND : angle 1.35758 / 0.90 ( 98) hydrogen bonds : bond 0.03055 / 2.03 ( 1185) hydrogen bonds : angle 5.13059 / 3.60 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 397 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8416 (tttt) REVERT: A 347 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8361 (mttp) REVERT: A 351 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8329 (mtpp) REVERT: A 366 LYS cc_start: 0.8552 (ptmt) cc_final: 0.8102 (ptpp) REVERT: A 396 ASN cc_start: 0.9180 (t0) cc_final: 0.8940 (t0) REVERT: A 397 GLN cc_start: 0.8289 (tt0) cc_final: 0.7881 (tt0) REVERT: B 36 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8097 (ttpp) REVERT: B 120 SER cc_start: 0.8765 (m) cc_final: 0.8426 (t) REVERT: B 214 ASP cc_start: 0.6641 (m-30) cc_final: 0.5913 (t0) REVERT: B 215 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8205 (tttt) REVERT: B 285 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7301 (mmm160) REVERT: C 112 MET cc_start: 0.5361 (pmt) cc_final: 0.4671 (tmm) REVERT: C 142 MET cc_start: 0.7052 (mmm) cc_final: 0.6803 (mmm) REVERT: C 162 LYS cc_start: 0.7218 (mtpt) cc_final: 0.6858 (tttp) REVERT: E 75 ASP cc_start: 0.9383 (OUTLIER) cc_final: 0.8975 (m-30) REVERT: E 79 LYS cc_start: 0.8479 (mttt) cc_final: 0.8059 (tptm) REVERT: E 115 LYS cc_start: 0.9100 (mtmm) cc_final: 0.8713 (mtmm) REVERT: E 133 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8895 (mm) REVERT: E 145 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8435 (mp0) REVERT: E 297 THR cc_start: 0.8876 (p) cc_final: 0.8575 (p) REVERT: E 321 LYS cc_start: 0.8356 (mtmm) cc_final: 0.8044 (ptpp) REVERT: E 366 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8330 (ttpp) REVERT: F 36 LYS cc_start: 0.8621 (tttp) cc_final: 0.8416 (ttmt) REVERT: F 120 SER cc_start: 0.8691 (m) cc_final: 0.8247 (p) REVERT: F 290 HIS cc_start: 0.9143 (OUTLIER) cc_final: 0.8582 (p-80) REVERT: F 353 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7933 (mt-10) REVERT: F 361 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7271 (pp) REVERT: G 142 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6953 (mpp) REVERT: G 216 LYS cc_start: 0.8169 (tptt) cc_final: 0.7769 (tptp) REVERT: I 79 LYS cc_start: 0.8251 (mttt) cc_final: 0.7896 (mtpp) REVERT: I 147 PHE cc_start: 0.8487 (m-80) cc_final: 0.8186 (m-10) REVERT: I 242 TYR cc_start: 0.8581 (m-10) cc_final: 0.8343 (m-80) REVERT: I 366 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7939 (ttpt) REVERT: J 28 CYS cc_start: 0.8249 (p) cc_final: 0.7082 (t) REVERT: J 79 LYS cc_start: 0.8586 (mttt) cc_final: 0.8322 (mtmm) REVERT: J 97 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8670 (ttp) REVERT: J 169 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.7894 (mpt) REVERT: J 250 ARG cc_start: 0.8711 (ptt90) cc_final: 0.8444 (ptt-90) REVERT: J 298 SER cc_start: 0.9015 (t) cc_final: 0.8797 (m) REVERT: J 376 MET cc_start: 0.7834 (mmm) cc_final: 0.7569 (ttp) REVERT: J 390 THR cc_start: 0.7883 (m) cc_final: 0.7606 (m) REVERT: J 393 ARG cc_start: 0.5878 (ttp-170) cc_final: 0.5449 (mtp-110) REVERT: K 114 MET cc_start: 0.6324 (mpt) cc_final: 0.6071 (ptt) REVERT: K 163 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7040 (ptmm) REVERT: M 75 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8828 (t0) REVERT: M 79 LYS cc_start: 0.8612 (mttt) cc_final: 0.8137 (mttp) REVERT: M 130 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8407 (tttm) REVERT: M 384 LYS cc_start: 0.8449 (mmtm) cc_final: 0.7983 (mmtt) REVERT: N 344 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: N 366 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8565 (m) REVERT: O 179 LYS cc_start: 0.6697 (mtmt) cc_final: 0.5990 (tptt) outliers start: 99 outliers final: 80 residues processed: 468 average time/residue: 0.1932 time to fit residues: 147.1042 Evaluate side-chains 483 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 390 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 366 LYS Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain M residue 73 GLN Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 302 GLN Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 344 GLU Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 210 ILE Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain Z residue 139 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 367 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 208 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 400 optimal weight: 10.0000 chunk 307 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN E 264 ASN F 287 HIS ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 94 HIS ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.157278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115359 restraints weight = 36505.488| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.03 r_work: 0.2939 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 32649 Z= 0.220 Angle : 0.598 10.811 44497 Z= 0.312 Chirality : 0.047 0.210 4975 Planarity : 0.005 0.051 5721 Dihedral : 5.392 58.411 4491 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 2.86 % Allowed : 13.64 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4110 helix: 2.12 (0.24), residues: 476 sheet: -0.43 (0.14), residues: 1272 loop : -0.57 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 251 TYR 0.027 0.002 TYR A 137 PHE 0.017 0.002 PHE I 13 TRP 0.011 0.001 TRP K 268 HIS 0.010 0.001 HIS E 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.22 (32600) covalent geometry : angle 0.59512 / 0.31 (44399) SS BOND : bond 0.00478 / 0.28 ( 49) SS BOND : angle 1.41351 / 0.94 ( 98) hydrogen bonds : bond 0.03236 / 2.15 ( 1185) hydrogen bonds : angle 5.24586 / 3.67 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10289.96 seconds wall clock time: 176 minutes 48.24 seconds (10608.24 seconds total)