Starting phenix.real_space_refine on Fri Jun 27 08:35:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eau_47846/06_2025/9eau_47846.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eau_47846/06_2025/9eau_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_47846/06_2025/9eau_47846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eau_47846/06_2025/9eau_47846.map" model { file = "/net/cci-nas-00/data/ceres_data/9eau_47846/06_2025/9eau_47846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eau_47846/06_2025/9eau_47846.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.72, per 1000 atoms: 0.56 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: 6.76 Conformation dependent library (CDL) restraints added in 3.6 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: 5.11 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: 12.57 Time building geometry restraints manager: 8.23 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 2.510 ... (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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 68.330 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 2.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (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 TRP 0.032 0.002 TRP C 268 HIS 0.012 0.001 HIS F 146 PHE 0.019 0.002 PHE J 313 TYR 0.038 0.005 TYR J 110 ARG 0.020 0.003 ARG F 271 Details of bonding type rmsd hydrogen bonds : bond 0.16047 ( 1185) hydrogen bonds : angle 8.04725 ( 3162) SS BOND : bond 0.00290 ( 49) SS BOND : angle 1.47742 ( 98) covalent geometry : bond 0.00401 (32600) covalent geometry : angle 0.73286 (44399) *********************** 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 : 3.117 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: 0.4712 time to fit residues: 505.8997 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 : 3.669 ------------------------------------------------------------------------------- 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 339 optimal weight: 8.9990 chunk 304 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 315 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 234 optimal weight: 0.9980 chunk 365 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS B 104 HIS B 236 GLN B 331 ASN C 198 HIS E 18 HIS E 102 GLN E 333 HIS F 104 HIS ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN G 195 ASN G 197 HIS I 18 HIS I 102 GLN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 99 HIS J 104 HIS J 236 GLN J 287 HIS M 18 HIS 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 287 HIS N 331 ASN Y 138 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112423 restraints weight = 36284.870| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.89 r_work: 0.3028 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 32649 Z= 0.222 Angle : 0.672 10.473 44497 Z= 0.359 Chirality : 0.049 0.214 4975 Planarity : 0.004 0.047 5721 Dihedral : 6.931 59.907 4531 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 2.75 % Allowed : 8.24 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4110 helix: 1.04 (0.23), residues: 452 sheet: -0.01 (0.15), residues: 1144 loop : -0.47 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 268 HIS 0.009 0.001 HIS I 308 PHE 0.016 0.002 PHE F 241 TYR 0.026 0.002 TYR F 199 ARG 0.005 0.001 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 1185) hydrogen bonds : angle 6.01606 ( 3162) SS BOND : bond 0.00892 ( 49) SS BOND : angle 1.72108 ( 98) covalent geometry : bond 0.00546 (32600) covalent geometry : angle 0.66760 (44399) *********************** 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 566 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 470 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8718 (t) cc_final: 0.8274 (m) REVERT: A 32 GLU cc_start: 0.8422 (tt0) cc_final: 0.7998 (tt0) REVERT: A 130 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7686 (tttp) REVERT: A 160 LYS cc_start: 0.7754 (mttt) cc_final: 0.7525 (mttp) REVERT: A 171 SER cc_start: 0.8577 (p) cc_final: 0.8278 (t) REVERT: A 344 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7832 (m) REVERT: A 347 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8014 (mttp) REVERT: A 366 LYS cc_start: 0.7872 (ptmt) cc_final: 0.7669 (ptpp) REVERT: A 396 ASN cc_start: 0.8796 (t0) cc_final: 0.8566 (t0) REVERT: A 397 GLN cc_start: 0.8049 (tt0) cc_final: 0.7654 (tt0) REVERT: A 436 MET cc_start: 0.6937 (tpp) cc_final: 0.6695 (mmm) REVERT: B 36 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7831 (ttpp) REVERT: B 61 THR cc_start: 0.8420 (m) cc_final: 0.8026 (t) REVERT: B 120 SER cc_start: 0.7887 (m) cc_final: 0.7591 (t) REVERT: B 130 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8721 (tptp) REVERT: B 142 VAL cc_start: 0.4322 (OUTLIER) cc_final: 0.3752 (t) REVERT: B 199 TYR cc_start: 0.8066 (p90) cc_final: 0.7856 (p90) REVERT: B 203 CYS cc_start: 0.4534 (OUTLIER) cc_final: 0.4178 (p) REVERT: B 214 ASP cc_start: 0.6264 (m-30) cc_final: 0.5502 (t0) REVERT: B 215 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7721 (tttt) REVERT: B 265 CYS cc_start: 0.8396 (t) cc_final: 0.7768 (m) REVERT: B 285 ARG cc_start: 0.7743 (mtt180) cc_final: 0.6557 (mmm160) REVERT: B 315 GLU cc_start: 0.8723 (tt0) cc_final: 0.8428 (tt0) REVERT: C 112 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.4057 (tmm) REVERT: C 114 MET cc_start: 0.6519 (mpt) cc_final: 0.6095 (mpt) REVERT: C 162 LYS cc_start: 0.6766 (mtpt) cc_final: 0.6333 (ttpp) REVERT: E 79 LYS cc_start: 0.8273 (mttt) cc_final: 0.7499 (tptm) REVERT: E 115 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8629 (mtmm) REVERT: E 145 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8108 (mp0) REVERT: E 321 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7583 (mttm) REVERT: E 341 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: E 345 LYS cc_start: 0.8595 (mttt) cc_final: 0.8260 (mmmt) REVERT: E 366 LYS cc_start: 0.8676 (mtpt) cc_final: 0.7565 (ttpp) REVERT: E 401 ASP cc_start: 0.7981 (t70) cc_final: 0.7468 (t0) REVERT: E 402 MET cc_start: 0.8104 (mmt) cc_final: 0.7637 (mmt) REVERT: F 4 GLU cc_start: 0.7910 (pt0) cc_final: 0.7254 (pm20) REVERT: F 36 LYS cc_start: 0.8612 (tttp) cc_final: 0.8106 (ttmt) REVERT: F 70 MET cc_start: 0.8902 (mmm) cc_final: 0.8628 (mmt) REVERT: F 81 ASP cc_start: 0.8355 (t0) cc_final: 0.8122 (m-30) REVERT: F 120 SER cc_start: 0.8029 (m) cc_final: 0.7607 (p) REVERT: F 250 ARG cc_start: 0.8488 (ptt90) cc_final: 0.8145 (ptt180) REVERT: F 353 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7030 (mt-10) REVERT: F 401 LEU cc_start: 0.6194 (mp) cc_final: 0.5946 (mt) REVERT: I 7 ILE cc_start: 0.7845 (pt) cc_final: 0.7546 (pt) REVERT: I 79 LYS cc_start: 0.7955 (mttt) cc_final: 0.7369 (mmmt) REVERT: I 147 PHE cc_start: 0.8157 (m-80) cc_final: 0.7760 (m-10) REVERT: I 160 LYS cc_start: 0.7731 (mttt) cc_final: 0.7492 (mmmt) REVERT: I 366 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7167 (ttpt) REVERT: I 373 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8356 (mttm) REVERT: J 4 GLU cc_start: 0.8469 (tt0) cc_final: 0.7631 (tp30) REVERT: J 28 CYS cc_start: 0.7972 (t) cc_final: 0.6980 (p) REVERT: J 79 LYS cc_start: 0.8421 (mttt) cc_final: 0.8003 (mttp) REVERT: J 169 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.7395 (mpt) REVERT: J 250 ARG cc_start: 0.8605 (ptt90) cc_final: 0.8266 (ptt-90) REVERT: J 298 SER cc_start: 0.9149 (t) cc_final: 0.8824 (m) REVERT: J 356 GLN cc_start: 0.7858 (mt0) cc_final: 0.7650 (mt0) REVERT: J 376 MET cc_start: 0.7457 (mmm) cc_final: 0.6946 (ttt) REVERT: J 390 THR cc_start: 0.7100 (m) cc_final: 0.6894 (m) REVERT: J 393 ARG cc_start: 0.5127 (ttp-170) cc_final: 0.4781 (mtp-110) REVERT: K 114 MET cc_start: 0.6377 (mpt) cc_final: 0.6111 (ptt) REVERT: K 163 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6319 (pttp) REVERT: K 178 MET cc_start: 0.8150 (mpp) cc_final: 0.7932 (mmt) REVERT: M 3 HIS cc_start: 0.7902 (t-90) cc_final: 0.7515 (t-170) REVERT: M 75 ASP cc_start: 0.9332 (OUTLIER) cc_final: 0.8894 (t0) REVERT: M 79 LYS cc_start: 0.8498 (mttt) cc_final: 0.7534 (mmmt) REVERT: M 115 LYS cc_start: 0.8944 (tttt) cc_final: 0.8569 (ttpp) REVERT: M 142 GLN cc_start: 0.8309 (tt0) cc_final: 0.7725 (tt0) REVERT: M 145 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8419 (mp0) REVERT: M 245 LYS cc_start: 0.8486 (pttm) cc_final: 0.8184 (mtpp) REVERT: M 373 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8246 (mtpt) REVERT: M 397 GLN cc_start: 0.8554 (tt0) cc_final: 0.8275 (tt0) REVERT: M 402 MET cc_start: 0.8567 (mmt) cc_final: 0.8269 (mmm) REVERT: N 76 GLN cc_start: 0.8306 (mt0) cc_final: 0.7893 (mm-40) REVERT: N 200 ASN cc_start: 0.6091 (t0) cc_final: 0.5704 (t0) REVERT: N 221 LYS cc_start: 0.7171 (mmtp) cc_final: 0.6755 (mtmt) REVERT: N 302 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8396 (mm-30) REVERT: O 125 LYS cc_start: 0.7102 (tttp) cc_final: 0.6860 (tmtt) REVERT: O 179 LYS cc_start: 0.6717 (mtmt) cc_final: 0.6126 (tptt) outliers start: 96 outliers final: 50 residues processed: 539 average time/residue: 0.4433 time to fit residues: 375.0736 Evaluate side-chains 482 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 421 time to evaluate : 3.287 ------------------------------------------------------------------------------- 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 344 VAL Chi-restraints excluded: chain A residue 346 VAL 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 130 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 298 SER Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 112 MET 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 249 SER Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 276 THR 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 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 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 75 ASP Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 285 SER 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 179 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain O residue 147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 104 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 chunk 312 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 297 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 364 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 chunk 274 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS B 332 ASN E 411 GLN F 94 HIS F 104 HIS ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 ASN J 236 GLN J 331 ASN M 155 ASN N 104 HIS N 236 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.164391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115094 restraints weight = 36416.378| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.89 r_work: 0.3074 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32649 Z= 0.124 Angle : 0.552 10.823 44497 Z= 0.293 Chirality : 0.045 0.179 4975 Planarity : 0.004 0.042 5721 Dihedral : 5.986 59.380 4510 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 2.72 % Allowed : 9.53 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4110 helix: 1.80 (0.23), residues: 452 sheet: -0.14 (0.14), residues: 1286 loop : -0.37 (0.13), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 268 HIS 0.021 0.001 HIS O 177 PHE 0.011 0.001 PHE F 115 TYR 0.023 0.001 TYR F 199 ARG 0.006 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 1185) hydrogen bonds : angle 5.52394 ( 3162) SS BOND : bond 0.00639 ( 49) SS BOND : angle 1.15658 ( 98) covalent geometry : bond 0.00286 (32600) covalent geometry : angle 0.55005 (44399) *********************** 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 555 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 460 time to evaluate : 3.847 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: 0.8836 (t) cc_final: 0.8477 (m) REVERT: A 130 LYS cc_start: 0.8306 (ttpp) cc_final: 0.7771 (tttt) REVERT: A 160 LYS cc_start: 0.7910 (mttt) cc_final: 0.7592 (mttp) REVERT: A 183 ASP cc_start: 0.8286 (m-30) cc_final: 0.8045 (m-30) REVERT: A 344 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7819 (m) REVERT: A 347 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8101 (mttp) REVERT: A 366 LYS cc_start: 0.7984 (ptmt) cc_final: 0.7171 (pttt) REVERT: A 397 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: A 402 MET cc_start: 0.7859 (mmt) cc_final: 0.7254 (mmt) REVERT: B 36 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.7993 (ttpp) REVERT: B 58 LYS cc_start: 0.8384 (mtpt) cc_final: 0.7941 (mtmt) REVERT: B 61 THR cc_start: 0.8449 (m) cc_final: 0.8143 (t) REVERT: B 76 GLN cc_start: 0.8095 (mt0) cc_final: 0.7664 (mm-40) REVERT: B 120 SER cc_start: 0.7982 (m) cc_final: 0.7659 (t) REVERT: B 130 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8736 (tptp) REVERT: B 199 TYR cc_start: 0.8039 (p90) cc_final: 0.7696 (p90) REVERT: B 203 CYS cc_start: 0.4123 (OUTLIER) cc_final: 0.3773 (p) REVERT: B 214 ASP cc_start: 0.6500 (m-30) cc_final: 0.5578 (t0) REVERT: B 215 LYS cc_start: 0.8232 (ttpt) cc_final: 0.7977 (ttpt) REVERT: B 265 CYS cc_start: 0.8345 (t) cc_final: 0.7893 (m) REVERT: B 285 ARG cc_start: 0.7807 (mtt180) cc_final: 0.6742 (mmm160) REVERT: B 315 GLU cc_start: 0.8703 (tt0) cc_final: 0.8431 (tt0) REVERT: B 322 GLU cc_start: 0.8060 (tp30) cc_final: 0.7823 (pt0) REVERT: C 112 MET cc_start: 0.5572 (pmt) cc_final: 0.4013 (tmm) REVERT: C 114 MET cc_start: 0.6716 (mpt) cc_final: 0.6045 (mpt) REVERT: C 162 LYS cc_start: 0.6717 (mtpt) cc_final: 0.6309 (tttp) REVERT: E 79 LYS cc_start: 0.8321 (mttt) cc_final: 0.7593 (tptm) REVERT: E 145 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8204 (mp0) REVERT: E 211 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8144 (mmtm) REVERT: E 321 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7866 (mttm) REVERT: E 345 LYS cc_start: 0.8614 (mttt) cc_final: 0.8327 (mmmt) REVERT: E 366 LYS cc_start: 0.8785 (mtpt) cc_final: 0.7679 (ttpp) REVERT: E 401 ASP cc_start: 0.7986 (t70) cc_final: 0.7562 (t0) REVERT: E 402 MET cc_start: 0.8078 (mmt) cc_final: 0.7668 (mmt) REVERT: F 4 GLU cc_start: 0.7906 (pt0) cc_final: 0.7291 (pm20) REVERT: F 36 LYS cc_start: 0.8572 (tttp) cc_final: 0.8095 (ttmt) REVERT: F 70 MET cc_start: 0.8837 (mmm) cc_final: 0.8603 (mmt) REVERT: F 120 SER cc_start: 0.7981 (m) cc_final: 0.7526 (p) REVERT: F 250 ARG cc_start: 0.8598 (ptt90) cc_final: 0.8274 (ptt180) REVERT: F 290 HIS cc_start: 0.9194 (OUTLIER) cc_final: 0.8641 (p-80) REVERT: F 353 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7168 (mt-10) REVERT: I 7 ILE cc_start: 0.7889 (pt) cc_final: 0.7528 (pt) REVERT: I 79 LYS cc_start: 0.8014 (mttt) cc_final: 0.7331 (mmmt) REVERT: I 147 PHE cc_start: 0.8208 (m-80) cc_final: 0.7887 (m-10) REVERT: I 373 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8154 (mtpt) REVERT: J 4 GLU cc_start: 0.8487 (tt0) cc_final: 0.7661 (tp30) REVERT: J 28 CYS cc_start: 0.8094 (t) cc_final: 0.7217 (p) REVERT: J 32 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8152 (p) REVERT: J 79 LYS cc_start: 0.8525 (mttt) cc_final: 0.8123 (mttp) REVERT: J 169 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.7464 (mpt) REVERT: J 298 SER cc_start: 0.9177 (t) cc_final: 0.8823 (m) REVERT: J 356 GLN cc_start: 0.8005 (mt0) cc_final: 0.7792 (mt0) REVERT: J 376 MET cc_start: 0.7455 (mmm) cc_final: 0.7015 (ttt) REVERT: J 393 ARG cc_start: 0.5146 (ttp-170) cc_final: 0.4764 (mtp-110) REVERT: K 114 MET cc_start: 0.6371 (mpt) cc_final: 0.6129 (ptt) REVERT: K 163 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6439 (pttp) REVERT: K 178 MET cc_start: 0.7877 (mpp) cc_final: 0.7584 (mmt) REVERT: M 3 HIS cc_start: 0.7983 (t-90) cc_final: 0.7763 (t-90) REVERT: M 75 ASP cc_start: 0.9322 (OUTLIER) cc_final: 0.9016 (t0) REVERT: M 79 LYS cc_start: 0.8540 (mttt) cc_final: 0.7760 (mmmt) REVERT: M 115 LYS cc_start: 0.8945 (tttt) cc_final: 0.8614 (ttpp) REVERT: M 133 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8865 (mm) REVERT: M 142 GLN cc_start: 0.8152 (tt0) cc_final: 0.7755 (tt0) REVERT: M 145 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8410 (mp0) REVERT: M 245 LYS cc_start: 0.8519 (pttm) cc_final: 0.8224 (mtpp) REVERT: M 344 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8272 (p) REVERT: M 373 LYS cc_start: 0.8625 (mtmm) cc_final: 0.8298 (mtpt) REVERT: M 397 GLN cc_start: 0.8496 (tt0) cc_final: 0.8236 (tt0) REVERT: M 402 MET cc_start: 0.8627 (mmt) cc_final: 0.8305 (mmm) REVERT: N 76 GLN cc_start: 0.8313 (mt0) cc_final: 0.7875 (mm110) REVERT: N 199 TYR cc_start: 0.8087 (p90) cc_final: 0.7887 (p90) REVERT: N 302 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8322 (mm-30) REVERT: N 376 MET cc_start: 0.6947 (mmm) cc_final: 0.6705 (mmt) REVERT: O 179 LYS cc_start: 0.6626 (mtmt) cc_final: 0.6102 (tptt) outliers start: 95 outliers final: 53 residues processed: 529 average time/residue: 0.4582 time to fit residues: 383.6811 Evaluate side-chains 476 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 411 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP 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 344 VAL 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 78 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 191 THR 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 313 PHE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 232 VAL 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 344 VAL 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 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 129 LEU 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 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 290 HIS 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 245 THR 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 234 THR Chi-restraints excluded: chain M residue 344 VAL 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 179 THR Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 394 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 11 optimal weight: 0.0070 chunk 383 optimal weight: 8.9990 chunk 268 optimal weight: 7.9990 chunk 275 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 396 ASN B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN F 146 HIS F 331 ASN I 30 GLN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN J 104 HIS J 226 HIS J 236 GLN M 155 ASN ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110449 restraints weight = 36466.550| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.88 r_work: 0.2998 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 32649 Z= 0.261 Angle : 0.638 11.313 44497 Z= 0.336 Chirality : 0.049 0.208 4975 Planarity : 0.005 0.053 5721 Dihedral : 5.912 59.080 4501 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.79 % Rotamer: Outliers : 3.55 % Allowed : 10.55 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 4110 helix: 1.79 (0.24), residues: 452 sheet: -0.27 (0.14), residues: 1236 loop : -0.46 (0.13), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 268 HIS 0.010 0.001 HIS I 308 PHE 0.016 0.002 PHE M 163 TYR 0.023 0.002 TYR F 199 ARG 0.006 0.001 ARG F 178 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 1185) hydrogen bonds : angle 5.56661 ( 3162) SS BOND : bond 0.00579 ( 49) SS BOND : angle 1.36492 ( 98) covalent geometry : bond 0.00645 (32600) covalent geometry : angle 0.63513 (44399) *********************** 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 547 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 423 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8875 (t) cc_final: 0.8596 (m) REVERT: A 32 GLU cc_start: 0.8441 (tt0) cc_final: 0.8033 (tt0) REVERT: A 130 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7763 (tttt) REVERT: A 160 LYS cc_start: 0.7932 (mttt) cc_final: 0.7611 (mttp) REVERT: A 347 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8089 (mttp) REVERT: A 366 LYS cc_start: 0.7988 (ptmt) cc_final: 0.7496 (ptpp) REVERT: A 397 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: B 13 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7689 (ptp-170) REVERT: B 61 THR cc_start: 0.8461 (m) cc_final: 0.8162 (t) REVERT: B 84 ARG cc_start: 0.8765 (mtt90) cc_final: 0.8488 (mmt-90) REVERT: B 120 SER cc_start: 0.8082 (m) cc_final: 0.7683 (t) REVERT: B 130 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8701 (tptp) REVERT: B 203 CYS cc_start: 0.4021 (OUTLIER) cc_final: 0.3677 (p) REVERT: B 214 ASP cc_start: 0.6400 (m-30) cc_final: 0.5602 (t0) REVERT: B 215 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7996 (ttpt) REVERT: B 265 CYS cc_start: 0.8510 (t) cc_final: 0.7794 (m) REVERT: B 285 ARG cc_start: 0.7845 (mtt180) cc_final: 0.6773 (mmm160) REVERT: B 315 GLU cc_start: 0.8758 (tt0) cc_final: 0.8460 (tt0) REVERT: C 112 MET cc_start: 0.5536 (pmt) cc_final: 0.4004 (tmm) REVERT: C 162 LYS cc_start: 0.6744 (mtpt) cc_final: 0.6333 (tttp) REVERT: E 79 LYS cc_start: 0.8200 (mttt) cc_final: 0.7441 (tptm) REVERT: E 115 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8653 (mtmm) REVERT: E 145 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8269 (mp0) REVERT: E 345 LYS cc_start: 0.8661 (mttt) cc_final: 0.8333 (mmmt) REVERT: E 366 LYS cc_start: 0.8796 (mtpt) cc_final: 0.7643 (ttpp) REVERT: E 401 ASP cc_start: 0.7965 (t70) cc_final: 0.7481 (t0) REVERT: E 402 MET cc_start: 0.8106 (mmt) cc_final: 0.7701 (mmt) REVERT: F 4 GLU cc_start: 0.7950 (pt0) cc_final: 0.7248 (pm20) REVERT: F 36 LYS cc_start: 0.8573 (tttp) cc_final: 0.8101 (ttmt) REVERT: F 120 SER cc_start: 0.8320 (m) cc_final: 0.7829 (p) REVERT: F 250 ARG cc_start: 0.8584 (ptt90) cc_final: 0.8256 (ptt180) REVERT: F 290 HIS cc_start: 0.9240 (OUTLIER) cc_final: 0.8670 (p-80) REVERT: F 353 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7098 (mt-10) REVERT: F 361 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6959 (pp) REVERT: F 401 LEU cc_start: 0.6181 (mp) cc_final: 0.5934 (mt) REVERT: I 68 CYS cc_start: 0.8689 (p) cc_final: 0.7902 (t) REVERT: I 79 LYS cc_start: 0.7920 (mttt) cc_final: 0.7204 (mmmt) REVERT: I 147 PHE cc_start: 0.8183 (m-80) cc_final: 0.7810 (m-10) REVERT: I 366 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7229 (ttpt) REVERT: I 373 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8409 (mttm) REVERT: J 4 GLU cc_start: 0.8489 (tt0) cc_final: 0.7634 (tp30) REVERT: J 28 CYS cc_start: 0.8035 (t) cc_final: 0.7166 (p) REVERT: J 79 LYS cc_start: 0.8453 (mttt) cc_final: 0.8118 (mttp) REVERT: J 80 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7904 (tmt170) REVERT: J 169 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.7445 (mpt) REVERT: J 250 ARG cc_start: 0.8689 (ptt90) cc_final: 0.8049 (ptt-90) REVERT: J 298 SER cc_start: 0.9097 (t) cc_final: 0.8758 (m) REVERT: J 376 MET cc_start: 0.7491 (mmm) cc_final: 0.7055 (ttt) REVERT: J 393 ARG cc_start: 0.5179 (ttp-170) cc_final: 0.4817 (mtp-110) REVERT: K 114 MET cc_start: 0.6290 (mpt) cc_final: 0.6055 (ptt) REVERT: K 163 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6443 (pttp) REVERT: K 178 MET cc_start: 0.8002 (mpp) cc_final: 0.7598 (mmt) REVERT: M 75 ASP cc_start: 0.9391 (OUTLIER) cc_final: 0.9019 (t0) REVERT: M 79 LYS cc_start: 0.8528 (mttt) cc_final: 0.7720 (mmmt) REVERT: M 115 LYS cc_start: 0.8940 (tttt) cc_final: 0.8674 (ttpp) REVERT: M 133 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8945 (mm) REVERT: M 142 GLN cc_start: 0.8339 (tt0) cc_final: 0.7723 (tt0) REVERT: M 145 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8416 (mp0) REVERT: M 320 TYR cc_start: 0.8855 (p90) cc_final: 0.8638 (p90) REVERT: M 321 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7569 (mtpp) REVERT: M 373 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8322 (mtpt) REVERT: M 397 GLN cc_start: 0.8656 (tt0) cc_final: 0.8419 (tt0) REVERT: M 402 MET cc_start: 0.8692 (mmt) cc_final: 0.8368 (mmm) REVERT: N 76 GLN cc_start: 0.8359 (mt0) cc_final: 0.7861 (mm110) REVERT: N 366 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8104 (m) REVERT: O 179 LYS cc_start: 0.6518 (mtmt) cc_final: 0.5946 (tptt) outliers start: 124 outliers final: 75 residues processed: 514 average time/residue: 0.5595 time to fit residues: 460.2477 Evaluate side-chains 492 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 405 time to evaluate : 4.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 99 GLU 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 78 SER Chi-restraints excluded: chain B residue 130 LYS 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 E residue 29 LEU 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 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 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 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 297 THR 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 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 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 212 ASP Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 285 SER 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 208 VAL 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 115 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 351 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 396 ASN B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 HIS J 128 GLN J 236 GLN ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110887 restraints weight = 36087.394| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.80 r_work: 0.2989 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32649 Z= 0.217 Angle : 0.598 10.953 44497 Z= 0.315 Chirality : 0.047 0.224 4975 Planarity : 0.005 0.050 5721 Dihedral : 5.741 58.610 4498 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 3.35 % Allowed : 11.81 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4110 helix: 1.96 (0.24), residues: 452 sheet: -0.31 (0.14), residues: 1239 loop : -0.51 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 268 HIS 0.016 0.001 HIS A 230 PHE 0.015 0.002 PHE M 163 TYR 0.021 0.002 TYR A 137 ARG 0.005 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 1185) hydrogen bonds : angle 5.44709 ( 3162) SS BOND : bond 0.00639 ( 49) SS BOND : angle 1.26120 ( 98) covalent geometry : bond 0.00534 (32600) covalent geometry : angle 0.59543 (44399) *********************** 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 538 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 421 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8839 (t) cc_final: 0.8563 (m) REVERT: A 32 GLU cc_start: 0.8433 (tt0) cc_final: 0.7984 (tt0) REVERT: A 130 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7678 (tttt) REVERT: A 160 LYS cc_start: 0.7856 (mttt) cc_final: 0.7539 (mttp) REVERT: A 347 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8077 (mttp) REVERT: A 366 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7049 (pttt) REVERT: A 397 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: B 13 ARG cc_start: 0.8045 (mtm180) cc_final: 0.7629 (ptp-170) REVERT: B 61 THR cc_start: 0.8406 (m) cc_final: 0.8112 (t) REVERT: B 84 ARG cc_start: 0.8683 (mtt90) cc_final: 0.8393 (mmt-90) REVERT: B 120 SER cc_start: 0.7976 (m) cc_final: 0.7598 (t) REVERT: B 130 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8655 (tptp) REVERT: B 203 CYS cc_start: 0.4300 (OUTLIER) cc_final: 0.4023 (p) REVERT: B 214 ASP cc_start: 0.6323 (m-30) cc_final: 0.5540 (t0) REVERT: B 215 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7960 (ttpt) REVERT: B 265 CYS cc_start: 0.8413 (t) cc_final: 0.7724 (m) REVERT: B 285 ARG cc_start: 0.7788 (mtt180) cc_final: 0.6690 (mmm160) REVERT: B 315 GLU cc_start: 0.8707 (tt0) cc_final: 0.8349 (tt0) REVERT: B 411 LEU cc_start: 0.7446 (tp) cc_final: 0.7114 (mp) REVERT: C 112 MET cc_start: 0.5543 (pmt) cc_final: 0.4111 (tmm) REVERT: C 162 LYS cc_start: 0.6723 (mtpt) cc_final: 0.6320 (tttp) REVERT: E 79 LYS cc_start: 0.8160 (mttt) cc_final: 0.7297 (tptm) REVERT: E 115 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8624 (mtmm) REVERT: E 133 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8711 (mm) REVERT: E 145 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8270 (mp0) REVERT: E 320 TYR cc_start: 0.8812 (p90) cc_final: 0.8483 (p90) REVERT: E 345 LYS cc_start: 0.8625 (mttt) cc_final: 0.8283 (mmmt) REVERT: E 366 LYS cc_start: 0.8738 (mtpt) cc_final: 0.7544 (ttpp) REVERT: E 401 ASP cc_start: 0.7954 (t70) cc_final: 0.7448 (t0) REVERT: E 402 MET cc_start: 0.8109 (mmt) cc_final: 0.7725 (mmt) REVERT: E 436 MET cc_start: 0.2375 (OUTLIER) cc_final: 0.2001 (mpp) REVERT: F 4 GLU cc_start: 0.7905 (pt0) cc_final: 0.7226 (pm20) REVERT: F 36 LYS cc_start: 0.8539 (tttp) cc_final: 0.8044 (ttmt) REVERT: F 120 SER cc_start: 0.8324 (m) cc_final: 0.7858 (p) REVERT: F 290 HIS cc_start: 0.9215 (OUTLIER) cc_final: 0.8646 (p-80) REVERT: F 353 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6977 (mt-10) REVERT: G 216 LYS cc_start: 0.8157 (tptt) cc_final: 0.7701 (mmtm) REVERT: I 68 CYS cc_start: 0.8535 (p) cc_final: 0.8078 (t) REVERT: I 79 LYS cc_start: 0.7856 (mttt) cc_final: 0.7111 (mmmt) REVERT: I 147 PHE cc_start: 0.8151 (m-80) cc_final: 0.7775 (m-10) REVERT: I 366 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7244 (ttpt) REVERT: I 373 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8414 (mttm) REVERT: J 4 GLU cc_start: 0.8513 (tt0) cc_final: 0.7733 (tp30) REVERT: J 28 CYS cc_start: 0.7954 (t) cc_final: 0.7043 (p) REVERT: J 79 LYS cc_start: 0.8499 (mttt) cc_final: 0.8072 (mttp) REVERT: J 80 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7890 (tmt170) REVERT: J 97 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8563 (ttp) REVERT: J 169 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7383 (mpt) REVERT: J 298 SER cc_start: 0.9056 (t) cc_final: 0.8717 (m) REVERT: J 376 MET cc_start: 0.7433 (mmm) cc_final: 0.7098 (ttp) REVERT: J 390 THR cc_start: 0.7258 (m) cc_final: 0.7005 (m) REVERT: J 393 ARG cc_start: 0.5099 (ttp-170) cc_final: 0.4742 (mtp-110) REVERT: K 114 MET cc_start: 0.6299 (mpt) cc_final: 0.6063 (ptt) REVERT: K 163 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6522 (ptmm) REVERT: K 178 MET cc_start: 0.7926 (mpp) cc_final: 0.7486 (mmt) REVERT: M 75 ASP cc_start: 0.9349 (OUTLIER) cc_final: 0.9001 (t0) REVERT: M 79 LYS cc_start: 0.8449 (mttt) cc_final: 0.7711 (mttp) REVERT: M 115 LYS cc_start: 0.8906 (tttt) cc_final: 0.8626 (ttpp) REVERT: M 130 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8095 (tttm) REVERT: M 133 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8890 (mm) REVERT: M 135 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8499 (mm) REVERT: M 142 GLN cc_start: 0.8276 (tt0) cc_final: 0.7674 (tt0) REVERT: M 145 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8492 (mp0) REVERT: M 321 LYS cc_start: 0.7801 (mtpp) cc_final: 0.7526 (mtpp) REVERT: M 373 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8283 (mtpt) REVERT: M 397 GLN cc_start: 0.8592 (tt0) cc_final: 0.8328 (tt0) REVERT: M 402 MET cc_start: 0.8656 (mmt) cc_final: 0.8322 (mmm) REVERT: N 246 ASP cc_start: 0.8040 (p0) cc_final: 0.7797 (p0) REVERT: N 344 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: N 366 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.8032 (m) REVERT: O 179 LYS cc_start: 0.6452 (mtmt) cc_final: 0.5968 (tptt) outliers start: 117 outliers final: 79 residues processed: 503 average time/residue: 0.4324 time to fit residues: 348.3691 Evaluate side-chains 499 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 404 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 228 VAL 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 78 SER Chi-restraints excluded: chain B residue 130 LYS 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 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 133 ILE Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 344 VAL 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 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 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 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 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 361 LEU Chi-restraints excluded: chain J residue 366 THR 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 135 ILE 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 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 O residue 147 VAL Chi-restraints excluded: chain O residue 210 ILE Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 235 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 149 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 165 optimal weight: 0.0470 chunk 175 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 269 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 411 GLN F 226 HIS ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3811 r_free = 0.3811 target = 0.159848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111726 restraints weight = 36591.011| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.83 r_work: 0.3039 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32649 Z= 0.144 Angle : 0.548 10.556 44497 Z= 0.289 Chirality : 0.045 0.250 4975 Planarity : 0.004 0.049 5721 Dihedral : 5.530 59.962 4498 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.33 % Rotamer: Outliers : 3.12 % Allowed : 12.53 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4110 helix: 2.16 (0.24), residues: 452 sheet: -0.29 (0.14), residues: 1256 loop : -0.46 (0.13), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 268 HIS 0.017 0.001 HIS A 230 PHE 0.012 0.001 PHE M 163 TYR 0.022 0.001 TYR A 137 ARG 0.006 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 1185) hydrogen bonds : angle 5.26525 ( 3162) SS BOND : bond 0.00419 ( 49) SS BOND : angle 1.30774 ( 98) covalent geometry : bond 0.00344 (32600) covalent geometry : angle 0.54562 (44399) *********************** 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 545 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 436 time to evaluate : 3.277 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: 0.8893 (t) cc_final: 0.8643 (m) REVERT: A 32 GLU cc_start: 0.8464 (tt0) cc_final: 0.8043 (tt0) REVERT: A 130 LYS cc_start: 0.8369 (ttpp) cc_final: 0.7802 (tttt) REVERT: A 160 LYS cc_start: 0.7908 (mttt) cc_final: 0.7679 (mttp) REVERT: A 347 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8130 (mttp) REVERT: A 353 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8546 (t) REVERT: A 366 LYS cc_start: 0.8015 (ptmt) cc_final: 0.7524 (ptpp) REVERT: A 397 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: B 13 ARG cc_start: 0.8109 (mtm180) cc_final: 0.7702 (ptp-170) REVERT: B 36 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7910 (ttpp) REVERT: B 61 THR cc_start: 0.8479 (m) cc_final: 0.8222 (t) REVERT: B 76 GLN cc_start: 0.8175 (mt0) cc_final: 0.7713 (mm-40) REVERT: B 84 ARG cc_start: 0.8726 (mtt90) cc_final: 0.8424 (mmt-90) REVERT: B 120 SER cc_start: 0.8273 (m) cc_final: 0.7910 (t) REVERT: B 203 CYS cc_start: 0.4772 (OUTLIER) cc_final: 0.4517 (p) REVERT: B 214 ASP cc_start: 0.6311 (m-30) cc_final: 0.5478 (t0) REVERT: B 215 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8089 (ttpt) REVERT: B 265 CYS cc_start: 0.8344 (t) cc_final: 0.7891 (m) REVERT: B 285 ARG cc_start: 0.7816 (mtt180) cc_final: 0.6767 (mmm160) REVERT: B 315 GLU cc_start: 0.8720 (tt0) cc_final: 0.8420 (tt0) REVERT: C 112 MET cc_start: 0.5540 (pmt) cc_final: 0.4393 (tmm) REVERT: C 162 LYS cc_start: 0.6743 (mtpt) cc_final: 0.6314 (tttp) REVERT: E 66 SER cc_start: 0.8371 (t) cc_final: 0.8007 (p) REVERT: E 79 LYS cc_start: 0.8231 (mttt) cc_final: 0.7420 (tptm) REVERT: E 145 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8312 (mp0) REVERT: E 297 THR cc_start: 0.8765 (p) cc_final: 0.8429 (p) REVERT: E 320 TYR cc_start: 0.8838 (p90) cc_final: 0.8627 (p90) REVERT: E 321 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7719 (ptpp) REVERT: E 345 LYS cc_start: 0.8642 (mttt) cc_final: 0.8342 (mmmt) REVERT: E 366 LYS cc_start: 0.8808 (mtpt) cc_final: 0.7670 (ttpp) REVERT: E 397 GLN cc_start: 0.8583 (tt0) cc_final: 0.8254 (tt0) REVERT: E 401 ASP cc_start: 0.8019 (t70) cc_final: 0.7545 (t0) REVERT: E 402 MET cc_start: 0.8095 (mmt) cc_final: 0.7791 (mmt) REVERT: F 4 GLU cc_start: 0.7941 (pt0) cc_final: 0.7304 (pm20) REVERT: F 36 LYS cc_start: 0.8549 (tttp) cc_final: 0.8107 (ttmt) REVERT: F 120 SER cc_start: 0.8393 (m) cc_final: 0.7920 (p) REVERT: F 290 HIS cc_start: 0.9223 (OUTLIER) cc_final: 0.8643 (p-80) REVERT: F 353 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7100 (mt-10) REVERT: F 397 THR cc_start: 0.6306 (OUTLIER) cc_final: 0.5973 (m) REVERT: G 114 MET cc_start: 0.6334 (ptp) cc_final: 0.6091 (ptp) REVERT: G 216 LYS cc_start: 0.8173 (tptt) cc_final: 0.7689 (mmtm) REVERT: I 79 LYS cc_start: 0.7935 (mttt) cc_final: 0.7215 (mmmt) REVERT: I 147 PHE cc_start: 0.8218 (m-80) cc_final: 0.7848 (m-10) REVERT: I 151 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7723 (tt0) REVERT: I 366 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7284 (ttpt) REVERT: J 4 GLU cc_start: 0.8526 (tt0) cc_final: 0.7760 (tp30) REVERT: J 28 CYS cc_start: 0.7981 (t) cc_final: 0.7163 (p) REVERT: J 32 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8246 (p) REVERT: J 79 LYS cc_start: 0.8550 (mttt) cc_final: 0.8133 (mttp) REVERT: J 80 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7912 (tmt170) REVERT: J 97 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8638 (ttp) REVERT: J 169 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.7398 (mpt) REVERT: J 250 ARG cc_start: 0.8589 (ptt90) cc_final: 0.8016 (ptt-90) REVERT: J 298 SER cc_start: 0.9074 (t) cc_final: 0.8754 (m) REVERT: J 376 MET cc_start: 0.7469 (mmm) cc_final: 0.7060 (ttt) REVERT: J 390 THR cc_start: 0.7299 (m) cc_final: 0.7048 (m) REVERT: J 393 ARG cc_start: 0.5189 (ttp-170) cc_final: 0.4813 (mtp-110) REVERT: K 114 MET cc_start: 0.6293 (mpt) cc_final: 0.6063 (ptt) REVERT: K 163 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6680 (ptmm) REVERT: K 178 MET cc_start: 0.7882 (mpp) cc_final: 0.7458 (mmt) REVERT: M 75 ASP cc_start: 0.9285 (OUTLIER) cc_final: 0.8951 (t0) REVERT: M 79 LYS cc_start: 0.8503 (mttt) cc_final: 0.7801 (mttp) REVERT: M 115 LYS cc_start: 0.8932 (tttt) cc_final: 0.8668 (ttpp) REVERT: M 130 LYS cc_start: 0.8663 (ttpp) cc_final: 0.7987 (tttm) REVERT: M 133 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8906 (mm) REVERT: M 135 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8591 (mm) REVERT: M 142 GLN cc_start: 0.8331 (tt0) cc_final: 0.7747 (tt0) REVERT: M 145 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8445 (mp0) REVERT: M 321 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7624 (mtpp) REVERT: M 373 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8343 (mtpt) REVERT: M 397 GLN cc_start: 0.8584 (tt0) cc_final: 0.8346 (tt0) REVERT: M 402 MET cc_start: 0.8656 (mmt) cc_final: 0.8309 (mmm) REVERT: N 246 ASP cc_start: 0.8078 (p0) cc_final: 0.7818 (p0) REVERT: N 344 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: N 366 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8083 (m) REVERT: O 179 LYS cc_start: 0.6519 (mtmt) cc_final: 0.5934 (tptt) outliers start: 109 outliers final: 73 residues processed: 513 average time/residue: 0.4400 time to fit residues: 359.7811 Evaluate side-chains 494 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 404 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 VAL 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 353 THR Chi-restraints excluded: chain A residue 396 ASN 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 78 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 254 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 290 HIS 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 97 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 344 VAL 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 397 THR 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 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 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 133 ILE Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 212 ASP Chi-restraints excluded: chain M residue 234 THR 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 64 HIS 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 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 235 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 100 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 357 optimal weight: 0.8980 chunk 237 optimal weight: 0.0270 chunk 187 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 255 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 230 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.164022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115384 restraints weight = 36481.786| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.86 r_work: 0.3073 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32649 Z= 0.110 Angle : 0.519 10.155 44497 Z= 0.273 Chirality : 0.044 0.180 4975 Planarity : 0.004 0.047 5721 Dihedral : 5.279 59.941 4494 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 2.92 % Allowed : 12.76 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.13), residues: 4110 helix: 2.36 (0.24), residues: 452 sheet: -0.23 (0.14), residues: 1264 loop : -0.42 (0.13), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 268 HIS 0.009 0.001 HIS M 3 PHE 0.014 0.001 PHE I 13 TYR 0.025 0.001 TYR A 137 ARG 0.007 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 1185) hydrogen bonds : angle 5.09205 ( 3162) SS BOND : bond 0.00413 ( 49) SS BOND : angle 1.18871 ( 98) covalent geometry : bond 0.00255 (32600) covalent geometry : angle 0.51638 (44399) *********************** 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 541 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 439 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8851 (t) cc_final: 0.8610 (m) REVERT: A 32 GLU cc_start: 0.8387 (tt0) cc_final: 0.7997 (tt0) REVERT: A 130 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7689 (tttt) REVERT: A 160 LYS cc_start: 0.7799 (mttt) cc_final: 0.7349 (mmtp) REVERT: A 183 ASP cc_start: 0.8096 (m-30) cc_final: 0.7885 (m-30) REVERT: A 347 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8138 (mttp) REVERT: A 351 LYS cc_start: 0.8391 (ptpp) cc_final: 0.8093 (mtpp) REVERT: A 366 LYS cc_start: 0.7936 (ptmt) cc_final: 0.7455 (ptpp) REVERT: A 397 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: A 402 MET cc_start: 0.7797 (mmt) cc_final: 0.7175 (mmt) REVERT: B 13 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7784 (ptp-170) REVERT: B 36 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7873 (ttpp) REVERT: B 61 THR cc_start: 0.8389 (m) cc_final: 0.8139 (t) REVERT: B 76 GLN cc_start: 0.8086 (mt0) cc_final: 0.7639 (mm-40) REVERT: B 84 ARG cc_start: 0.8672 (mtt90) cc_final: 0.8380 (mmt-90) REVERT: B 203 CYS cc_start: 0.4514 (OUTLIER) cc_final: 0.4238 (p) REVERT: B 214 ASP cc_start: 0.6250 (m-30) cc_final: 0.5340 (t0) REVERT: B 215 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8049 (ttpt) REVERT: B 265 CYS cc_start: 0.8289 (t) cc_final: 0.7829 (m) REVERT: B 285 ARG cc_start: 0.7747 (mtt180) cc_final: 0.6661 (mmm160) REVERT: B 315 GLU cc_start: 0.8693 (tt0) cc_final: 0.8324 (tt0) REVERT: B 411 LEU cc_start: 0.7228 (mp) cc_final: 0.6882 (tt) REVERT: C 112 MET cc_start: 0.5623 (pmt) cc_final: 0.4567 (tmm) REVERT: C 142 MET cc_start: 0.6532 (mmm) cc_final: 0.6292 (mmm) REVERT: C 162 LYS cc_start: 0.6600 (mtpt) cc_final: 0.6191 (tttp) REVERT: C 179 LYS cc_start: 0.7111 (mtpt) cc_final: 0.6320 (mmmm) REVERT: E 75 ASP cc_start: 0.9464 (OUTLIER) cc_final: 0.9056 (m-30) REVERT: E 79 LYS cc_start: 0.8169 (mttt) cc_final: 0.7341 (tptm) REVERT: E 145 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8223 (mp0) REVERT: E 279 SER cc_start: 0.8730 (m) cc_final: 0.8357 (t) REVERT: E 297 THR cc_start: 0.8730 (p) cc_final: 0.8378 (p) REVERT: E 321 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7694 (ptpp) REVERT: E 345 LYS cc_start: 0.8625 (mttt) cc_final: 0.8309 (mmmt) REVERT: E 366 LYS cc_start: 0.8765 (mtpt) cc_final: 0.7774 (ttpp) REVERT: E 397 GLN cc_start: 0.8477 (tt0) cc_final: 0.8162 (tt0) REVERT: E 401 ASP cc_start: 0.7940 (t70) cc_final: 0.7488 (t0) REVERT: F 4 GLU cc_start: 0.7904 (pt0) cc_final: 0.7622 (mm-30) REVERT: F 36 LYS cc_start: 0.8478 (tttp) cc_final: 0.8023 (ttmt) REVERT: F 80 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7552 (tmt170) REVERT: F 120 SER cc_start: 0.8358 (m) cc_final: 0.7888 (p) REVERT: F 250 ARG cc_start: 0.8700 (ptt90) cc_final: 0.8322 (ptt180) REVERT: F 290 HIS cc_start: 0.9222 (OUTLIER) cc_final: 0.8618 (p-80) REVERT: F 353 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7042 (mt-10) REVERT: I 79 LYS cc_start: 0.7776 (mttt) cc_final: 0.6742 (tptp) REVERT: I 147 PHE cc_start: 0.8156 (m-80) cc_final: 0.7792 (m-10) REVERT: I 151 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7561 (tt0) REVERT: I 366 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7176 (ttpt) REVERT: J 4 GLU cc_start: 0.8631 (tt0) cc_final: 0.7936 (tp30) REVERT: J 28 CYS cc_start: 0.7920 (t) cc_final: 0.7066 (p) REVERT: J 70 MET cc_start: 0.8538 (tpp) cc_final: 0.8039 (tpp) REVERT: J 79 LYS cc_start: 0.8433 (mttt) cc_final: 0.7982 (mtmm) REVERT: J 97 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8620 (ttp) REVERT: J 169 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7306 (mpt) REVERT: J 250 ARG cc_start: 0.8540 (ptt90) cc_final: 0.8234 (ptt-90) REVERT: J 298 SER cc_start: 0.9038 (t) cc_final: 0.8717 (m) REVERT: J 376 MET cc_start: 0.7399 (mmm) cc_final: 0.6984 (ttt) REVERT: J 390 THR cc_start: 0.7175 (m) cc_final: 0.6927 (m) REVERT: J 393 ARG cc_start: 0.5045 (ttp-170) cc_final: 0.4666 (mtp-110) REVERT: K 114 MET cc_start: 0.6274 (mpt) cc_final: 0.6058 (ptt) REVERT: K 163 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6688 (ptmm) REVERT: M 75 ASP cc_start: 0.9251 (OUTLIER) cc_final: 0.8945 (t0) REVERT: M 79 LYS cc_start: 0.8420 (mttt) cc_final: 0.7695 (mttp) REVERT: M 115 LYS cc_start: 0.8888 (tttt) cc_final: 0.8614 (ttpp) REVERT: M 130 LYS cc_start: 0.8587 (ttpp) cc_final: 0.7895 (tttm) REVERT: M 133 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8833 (mm) REVERT: M 142 GLN cc_start: 0.8193 (tt0) cc_final: 0.7751 (tt0) REVERT: M 145 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8330 (mp0) REVERT: M 300 SER cc_start: 0.8865 (p) cc_final: 0.8590 (p) REVERT: M 321 LYS cc_start: 0.7803 (mtpp) cc_final: 0.7518 (mtpp) REVERT: M 373 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8256 (mtpt) REVERT: M 397 GLN cc_start: 0.8498 (tt0) cc_final: 0.8227 (tt0) REVERT: M 402 MET cc_start: 0.8553 (mmt) cc_final: 0.8208 (mmm) REVERT: N 344 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: O 142 MET cc_start: 0.7042 (mmt) cc_final: 0.6290 (mmm) REVERT: O 179 LYS cc_start: 0.6507 (mtmt) cc_final: 0.5938 (tptt) outliers start: 102 outliers final: 68 residues processed: 512 average time/residue: 0.4414 time to fit residues: 362.1129 Evaluate side-chains 494 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 412 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER 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 353 THR Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 48 ILE 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 276 THR 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 232 VAL Chi-restraints excluded: chain C residue 256 MET 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 249 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 80 ARG 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 G residue 135 CYS 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 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 13 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 155 SER 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 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 245 THR 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 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 208 VAL Chi-restraints excluded: chain N residue 344 GLU Chi-restraints excluded: chain N residue 361 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 99 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 chunk 382 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN 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 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 HIS ** J 146 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110955 restraints weight = 36370.757| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.88 r_work: 0.3003 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2925 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= 0.214 Angle : 0.589 11.311 44497 Z= 0.308 Chirality : 0.047 0.224 4975 Planarity : 0.004 0.051 5721 Dihedral : 5.430 58.800 4494 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 3.29 % Allowed : 13.19 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4110 helix: 2.27 (0.24), residues: 452 sheet: -0.28 (0.14), residues: 1256 loop : -0.50 (0.13), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 268 HIS 0.010 0.001 HIS I 308 PHE 0.017 0.002 PHE M 163 TYR 0.025 0.002 TYR A 137 ARG 0.007 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 1185) hydrogen bonds : angle 5.22331 ( 3162) SS BOND : bond 0.00498 ( 49) SS BOND : angle 1.42149 ( 98) covalent geometry : bond 0.00527 (32600) covalent geometry : angle 0.58604 (44399) *********************** 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 529 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 414 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8841 (t) cc_final: 0.8600 (m) REVERT: A 32 GLU cc_start: 0.8479 (tt0) cc_final: 0.8057 (tt0) REVERT: A 43 ASN cc_start: 0.8400 (m110) cc_final: 0.8185 (m110) REVERT: A 130 LYS cc_start: 0.8402 (ttpp) cc_final: 0.7843 (tttt) REVERT: A 160 LYS cc_start: 0.7882 (mttt) cc_final: 0.7428 (mmtp) REVERT: A 347 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8184 (mttp) REVERT: A 351 LYS cc_start: 0.8431 (ptpp) cc_final: 0.8170 (mtpp) REVERT: A 366 LYS cc_start: 0.7993 (ptmt) cc_final: 0.7525 (ptpp) REVERT: A 397 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: B 13 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7767 (ptp-170) REVERT: B 61 THR cc_start: 0.8456 (m) cc_final: 0.8196 (t) REVERT: B 84 ARG cc_start: 0.8738 (mtt90) cc_final: 0.8454 (mmt-90) REVERT: B 214 ASP cc_start: 0.6282 (m-30) cc_final: 0.5429 (t0) REVERT: B 215 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8080 (ttpt) REVERT: B 265 CYS cc_start: 0.8558 (t) cc_final: 0.7755 (m) REVERT: B 285 ARG cc_start: 0.7849 (mtt180) cc_final: 0.6776 (mmm160) REVERT: B 315 GLU cc_start: 0.8734 (tt0) cc_final: 0.8433 (tt0) REVERT: B 411 LEU cc_start: 0.7319 (mp) cc_final: 0.6947 (tt) REVERT: C 112 MET cc_start: 0.5646 (pmt) cc_final: 0.4693 (tmm) REVERT: C 162 LYS cc_start: 0.6674 (mtpt) cc_final: 0.6265 (tttp) REVERT: C 179 LYS cc_start: 0.7120 (mtpt) cc_final: 0.6309 (mmmm) REVERT: E 75 ASP cc_start: 0.9474 (OUTLIER) cc_final: 0.9093 (m-30) REVERT: E 79 LYS cc_start: 0.8274 (mttt) cc_final: 0.7401 (tptm) REVERT: E 133 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8780 (mm) REVERT: E 145 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8262 (mp0) REVERT: E 297 THR cc_start: 0.8735 (p) cc_final: 0.8370 (p) REVERT: E 321 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7645 (ptpp) REVERT: E 345 LYS cc_start: 0.8691 (mttt) cc_final: 0.8337 (mmmt) REVERT: E 366 LYS cc_start: 0.8808 (mtpt) cc_final: 0.7742 (ttpp) REVERT: E 397 GLN cc_start: 0.8547 (tt0) cc_final: 0.8239 (tt0) REVERT: E 401 ASP cc_start: 0.7967 (t70) cc_final: 0.7530 (t0) REVERT: F 36 LYS cc_start: 0.8544 (tttp) cc_final: 0.8123 (ttmt) REVERT: F 80 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7514 (tmt170) REVERT: F 120 SER cc_start: 0.8462 (m) cc_final: 0.7973 (p) REVERT: F 290 HIS cc_start: 0.9252 (OUTLIER) cc_final: 0.8656 (p-80) REVERT: F 353 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7071 (mt-10) REVERT: G 142 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6658 (mpp) REVERT: G 216 LYS cc_start: 0.8057 (tptt) cc_final: 0.7659 (tptp) REVERT: I 79 LYS cc_start: 0.7870 (mttt) cc_final: 0.7211 (mtpp) REVERT: I 147 PHE cc_start: 0.8287 (m-80) cc_final: 0.7926 (m-10) REVERT: I 151 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7669 (tt0) REVERT: I 366 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7260 (ttpt) REVERT: J 28 CYS cc_start: 0.7983 (t) cc_final: 0.7158 (p) REVERT: J 79 LYS cc_start: 0.8482 (mttt) cc_final: 0.8113 (mttp) REVERT: J 80 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7859 (tmt170) REVERT: J 97 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8594 (ttp) REVERT: J 169 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7352 (mpt) REVERT: J 250 ARG cc_start: 0.8571 (ptt90) cc_final: 0.7952 (ptt-90) REVERT: J 298 SER cc_start: 0.9077 (t) cc_final: 0.8747 (m) REVERT: J 376 MET cc_start: 0.7457 (mmm) cc_final: 0.7123 (ttp) REVERT: J 390 THR cc_start: 0.7268 (m) cc_final: 0.7015 (m) REVERT: J 393 ARG cc_start: 0.5222 (ttp-170) cc_final: 0.4827 (mtp-110) REVERT: K 114 MET cc_start: 0.6303 (mpt) cc_final: 0.6076 (ptt) REVERT: K 163 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6739 (ptmm) REVERT: M 75 ASP cc_start: 0.9310 (OUTLIER) cc_final: 0.8967 (t0) REVERT: M 79 LYS cc_start: 0.8471 (mttt) cc_final: 0.7773 (mttp) REVERT: M 115 LYS cc_start: 0.8935 (tttt) cc_final: 0.8672 (ttpp) REVERT: M 130 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8035 (tttm) REVERT: M 133 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8885 (mm) REVERT: M 135 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8554 (mm) REVERT: M 142 GLN cc_start: 0.8344 (tt0) cc_final: 0.7870 (tt0) REVERT: M 300 SER cc_start: 0.8855 (p) cc_final: 0.8587 (p) REVERT: M 321 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7633 (mtpp) REVERT: M 345 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8338 (mttt) REVERT: M 373 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8305 (mtpt) REVERT: M 397 GLN cc_start: 0.8626 (tt0) cc_final: 0.8377 (tt0) REVERT: N 344 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: O 142 MET cc_start: 0.7169 (mmt) cc_final: 0.6319 (mmm) REVERT: O 179 LYS cc_start: 0.6523 (mtmt) cc_final: 0.5917 (tptt) outliers start: 115 outliers final: 84 residues processed: 495 average time/residue: 0.4956 time to fit residues: 398.6244 Evaluate side-chains 504 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 404 time to evaluate : 3.808 ------------------------------------------------------------------------------- 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 188 ASP 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 353 THR Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 254 VAL 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 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 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 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 54 ILE Chi-restraints excluded: chain F residue 80 ARG 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 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 120 SER Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 236 THR 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 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 13 ARG 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 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 361 LEU Chi-restraints excluded: chain J residue 366 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 135 ILE 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 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 344 GLU Chi-restraints excluded: chain N residue 361 LEU 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 398 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 0.0050 chunk 86 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 346 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 HIS ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114036 restraints weight = 36321.089| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.84 r_work: 0.3063 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32649 Z= 0.120 Angle : 0.534 10.522 44497 Z= 0.279 Chirality : 0.045 0.195 4975 Planarity : 0.004 0.046 5721 Dihedral : 5.263 59.724 4493 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 2.89 % Allowed : 13.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4110 helix: 2.17 (0.24), residues: 476 sheet: -0.26 (0.14), residues: 1262 loop : -0.49 (0.13), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 409 HIS 0.008 0.001 HIS M 3 PHE 0.015 0.001 PHE I 13 TYR 0.026 0.001 TYR A 137 ARG 0.023 0.000 ARG E 412 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 1185) hydrogen bonds : angle 5.07038 ( 3162) SS BOND : bond 0.00316 ( 49) SS BOND : angle 1.28718 ( 98) covalent geometry : bond 0.00285 (32600) covalent geometry : angle 0.53104 (44399) *********************** 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 531 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 430 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8856 (t) cc_final: 0.8609 (m) REVERT: A 32 GLU cc_start: 0.8409 (tt0) cc_final: 0.7989 (tt0) REVERT: A 43 ASN cc_start: 0.8367 (m110) cc_final: 0.8162 (m110) REVERT: A 130 LYS cc_start: 0.8352 (ttpp) cc_final: 0.7725 (tttt) REVERT: A 160 LYS cc_start: 0.7802 (mttt) cc_final: 0.7374 (mmtp) REVERT: A 183 ASP cc_start: 0.8135 (m-30) cc_final: 0.7919 (m-30) REVERT: A 347 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8174 (mttp) REVERT: A 351 LYS cc_start: 0.8388 (ptpp) cc_final: 0.8167 (mtpp) REVERT: A 366 LYS cc_start: 0.7922 (ptmt) cc_final: 0.7466 (ptpp) REVERT: A 397 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: B 13 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7783 (ptp-170) REVERT: B 61 THR cc_start: 0.8402 (m) cc_final: 0.8145 (t) REVERT: B 76 GLN cc_start: 0.8130 (mt0) cc_final: 0.7675 (mm-40) REVERT: B 84 ARG cc_start: 0.8668 (mtt90) cc_final: 0.8373 (mmt-90) REVERT: B 214 ASP cc_start: 0.6144 (m-30) cc_final: 0.5308 (t0) REVERT: B 215 LYS cc_start: 0.8343 (ttpt) cc_final: 0.8054 (tttt) REVERT: B 265 CYS cc_start: 0.8302 (t) cc_final: 0.7820 (m) REVERT: B 285 ARG cc_start: 0.7754 (mtt180) cc_final: 0.6665 (mmm160) REVERT: B 315 GLU cc_start: 0.8664 (tt0) cc_final: 0.8345 (tt0) REVERT: B 411 LEU cc_start: 0.7273 (mp) cc_final: 0.6908 (tt) REVERT: C 112 MET cc_start: 0.5561 (pmt) cc_final: 0.4678 (tmm) REVERT: C 142 MET cc_start: 0.6574 (mmm) cc_final: 0.6338 (mmm) REVERT: C 162 LYS cc_start: 0.6626 (mtpt) cc_final: 0.6251 (tttp) REVERT: C 179 LYS cc_start: 0.7201 (mtpt) cc_final: 0.6417 (mmmm) REVERT: E 30 GLN cc_start: 0.8194 (mt0) cc_final: 0.7859 (tt0) REVERT: E 75 ASP cc_start: 0.9456 (OUTLIER) cc_final: 0.9095 (m-30) REVERT: E 79 LYS cc_start: 0.8201 (mttt) cc_final: 0.7305 (tptm) REVERT: E 145 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8200 (mp0) REVERT: E 297 THR cc_start: 0.8725 (p) cc_final: 0.8357 (p) REVERT: E 321 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7635 (ptpp) REVERT: E 345 LYS cc_start: 0.8648 (mttt) cc_final: 0.8168 (tptp) REVERT: E 366 LYS cc_start: 0.8754 (mtpt) cc_final: 0.7608 (ttpp) REVERT: E 397 GLN cc_start: 0.8503 (tt0) cc_final: 0.8152 (tt0) REVERT: E 401 ASP cc_start: 0.8003 (t70) cc_final: 0.7634 (t0) REVERT: F 4 GLU cc_start: 0.7922 (pt0) cc_final: 0.7609 (mm-30) REVERT: F 36 LYS cc_start: 0.8512 (tttp) cc_final: 0.8027 (ttmt) REVERT: F 80 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7557 (tmt170) REVERT: F 120 SER cc_start: 0.8407 (m) cc_final: 0.7888 (p) REVERT: F 250 ARG cc_start: 0.8695 (ptt90) cc_final: 0.8313 (ptt180) REVERT: F 290 HIS cc_start: 0.9227 (OUTLIER) cc_final: 0.8626 (p-80) REVERT: F 353 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7042 (mt-10) REVERT: G 142 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6554 (mpp) REVERT: G 216 LYS cc_start: 0.8089 (tptt) cc_final: 0.7694 (tptp) REVERT: I 79 LYS cc_start: 0.7835 (mttt) cc_final: 0.7127 (mtpp) REVERT: I 147 PHE cc_start: 0.8194 (m-80) cc_final: 0.7829 (m-10) REVERT: I 151 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7586 (tt0) REVERT: I 366 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7130 (ttpt) REVERT: J 28 CYS cc_start: 0.7929 (t) cc_final: 0.7072 (p) REVERT: J 70 MET cc_start: 0.8537 (tpp) cc_final: 0.8303 (tpp) REVERT: J 79 LYS cc_start: 0.8419 (mttt) cc_final: 0.7967 (mtmm) REVERT: J 80 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7893 (tmt170) REVERT: J 97 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8612 (ttp) REVERT: J 169 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7293 (mpt) REVERT: J 250 ARG cc_start: 0.8567 (ptt90) cc_final: 0.8257 (ptt-90) REVERT: J 298 SER cc_start: 0.9041 (t) cc_final: 0.8729 (m) REVERT: J 376 MET cc_start: 0.7386 (mmm) cc_final: 0.6967 (ttt) REVERT: J 390 THR cc_start: 0.7181 (m) cc_final: 0.6935 (m) REVERT: J 393 ARG cc_start: 0.5092 (ttp-170) cc_final: 0.4742 (mtp-110) REVERT: K 114 MET cc_start: 0.6285 (mpt) cc_final: 0.6038 (ptt) REVERT: K 163 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6721 (ptmm) REVERT: M 75 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8955 (t0) REVERT: M 79 LYS cc_start: 0.8437 (mttt) cc_final: 0.7682 (mttp) REVERT: M 115 LYS cc_start: 0.8897 (tttt) cc_final: 0.8630 (ttpp) REVERT: M 130 LYS cc_start: 0.8604 (ttpp) cc_final: 0.7954 (tttm) REVERT: M 133 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8849 (mm) REVERT: M 135 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8463 (mm) REVERT: M 142 GLN cc_start: 0.8246 (tt0) cc_final: 0.7806 (tt0) REVERT: M 300 SER cc_start: 0.8872 (p) cc_final: 0.8592 (p) REVERT: M 321 LYS cc_start: 0.7845 (mtpp) cc_final: 0.7558 (mtpp) REVERT: M 345 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8314 (mttt) REVERT: M 373 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8217 (mtpt) REVERT: M 397 GLN cc_start: 0.8505 (tt0) cc_final: 0.8233 (tt0) REVERT: M 399 PHE cc_start: 0.8777 (t80) cc_final: 0.8297 (t80) REVERT: N 344 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: O 142 MET cc_start: 0.7089 (mmt) cc_final: 0.6289 (mmm) REVERT: O 179 LYS cc_start: 0.6500 (mtmt) cc_final: 0.5884 (tptt) outliers start: 101 outliers final: 75 residues processed: 499 average time/residue: 0.4579 time to fit residues: 365.2410 Evaluate side-chains 503 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 413 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 188 ASP 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 353 THR Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 254 VAL 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 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 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 167 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 80 ARG 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 290 HIS Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 326 GLU 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 G residue 249 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 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 13 ARG 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 167 ILE 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 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 135 ILE 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 M residue 357 SER 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 N residue 191 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 344 GLU Chi-restraints excluded: chain N residue 361 LEU 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 303 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 366 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 chunk 323 optimal weight: 0.8980 chunk 368 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN E 340 GLN ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 HIS ** 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 = 0.3769 r_free = 0.3769 target = 0.160392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118745 restraints weight = 36622.387| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.07 r_work: 0.2990 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32649 Z= 0.115 Angle : 0.521 10.550 44497 Z= 0.272 Chirality : 0.044 0.176 4975 Planarity : 0.004 0.048 5721 Dihedral : 5.154 59.895 4493 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 2.80 % Allowed : 13.90 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.13), residues: 4110 helix: 2.33 (0.24), residues: 476 sheet: -0.25 (0.15), residues: 1261 loop : -0.46 (0.13), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 268 HIS 0.008 0.001 HIS M 3 PHE 0.015 0.001 PHE I 13 TYR 0.028 0.001 TYR A 137 ARG 0.007 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 1185) hydrogen bonds : angle 4.95879 ( 3162) SS BOND : bond 0.00287 ( 49) SS BOND : angle 1.20695 ( 98) covalent geometry : bond 0.00272 (32600) covalent geometry : angle 0.51872 (44399) ********************** 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 533 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 435 time to evaluate : 5.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8637 (tt0) cc_final: 0.8422 (tt0) REVERT: A 130 LYS cc_start: 0.8771 (ttpp) cc_final: 0.8373 (tttt) REVERT: A 160 LYS cc_start: 0.8435 (mttt) cc_final: 0.8132 (mmtp) REVERT: A 366 LYS cc_start: 0.8466 (ptmt) cc_final: 0.8010 (ptpp) REVERT: A 397 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: B 76 GLN cc_start: 0.8410 (mt0) cc_final: 0.8188 (mm-40) REVERT: B 214 ASP cc_start: 0.6632 (m-30) cc_final: 0.5944 (t0) REVERT: B 215 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8216 (tttt) REVERT: B 285 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7271 (mmm160) REVERT: B 315 GLU cc_start: 0.8637 (tt0) cc_final: 0.8427 (tt0) REVERT: B 411 LEU cc_start: 0.7816 (mp) cc_final: 0.7385 (tt) REVERT: C 112 MET cc_start: 0.5307 (pmt) cc_final: 0.4678 (tmm) REVERT: C 136 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6199 (mt) REVERT: C 142 MET cc_start: 0.7066 (mmm) cc_final: 0.6847 (mmm) REVERT: C 162 LYS cc_start: 0.7102 (mtpt) cc_final: 0.6793 (tttp) REVERT: C 179 LYS cc_start: 0.7634 (mtpt) cc_final: 0.6760 (mmmm) REVERT: E 30 GLN cc_start: 0.8459 (mt0) cc_final: 0.8253 (tt0) REVERT: E 75 ASP cc_start: 0.9386 (OUTLIER) cc_final: 0.9076 (m-30) REVERT: E 79 LYS cc_start: 0.8455 (mttt) cc_final: 0.8028 (tptm) REVERT: E 145 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8437 (mp0) REVERT: E 211 LYS cc_start: 0.8266 (mmtm) cc_final: 0.8034 (mmtm) REVERT: E 321 LYS cc_start: 0.8412 (mtmm) cc_final: 0.7965 (ptpp) REVERT: E 366 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8374 (ttpp) REVERT: E 397 GLN cc_start: 0.8658 (tt0) cc_final: 0.8436 (tt0) REVERT: E 411 GLN cc_start: 0.7587 (mt0) cc_final: 0.7353 (mt0) REVERT: F 80 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7904 (tmt170) REVERT: F 120 SER cc_start: 0.8615 (m) cc_final: 0.8150 (p) REVERT: F 250 ARG cc_start: 0.8910 (ptt90) cc_final: 0.8708 (ptt180) REVERT: F 290 HIS cc_start: 0.9152 (OUTLIER) cc_final: 0.8607 (p-80) REVERT: F 353 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7976 (mt-10) REVERT: F 401 LEU cc_start: 0.6645 (mp) cc_final: 0.6396 (mt) REVERT: G 142 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6790 (mpp) REVERT: G 216 LYS cc_start: 0.8244 (tptt) cc_final: 0.7862 (tptp) REVERT: I 79 LYS cc_start: 0.8250 (mttt) cc_final: 0.7862 (mtpp) REVERT: I 147 PHE cc_start: 0.8435 (m-80) cc_final: 0.8131 (m-10) REVERT: I 366 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7823 (ttpt) REVERT: J 79 LYS cc_start: 0.8597 (mttt) cc_final: 0.8325 (mtmm) REVERT: J 80 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8163 (tmt170) REVERT: J 97 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8620 (ttp) REVERT: J 169 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.7834 (mpt) REVERT: J 250 ARG cc_start: 0.8658 (ptt90) cc_final: 0.8238 (ptt-90) REVERT: J 298 SER cc_start: 0.8997 (t) cc_final: 0.8773 (m) REVERT: J 376 MET cc_start: 0.7796 (mmm) cc_final: 0.7556 (ttp) REVERT: J 390 THR cc_start: 0.7845 (m) cc_final: 0.7565 (m) REVERT: J 393 ARG cc_start: 0.5797 (ttp-170) cc_final: 0.5393 (mtp-110) REVERT: K 163 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7027 (ptmm) REVERT: M 75 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8830 (t0) REVERT: M 79 LYS cc_start: 0.8635 (mttt) cc_final: 0.8116 (mttp) REVERT: M 130 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8412 (tttm) REVERT: M 133 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9073 (mm) REVERT: M 142 GLN cc_start: 0.8311 (tt0) cc_final: 0.7977 (tt0) REVERT: M 321 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7909 (mtpp) REVERT: M 399 PHE cc_start: 0.8782 (t80) cc_final: 0.8343 (t80) REVERT: N 344 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: O 142 MET cc_start: 0.7538 (mmt) cc_final: 0.6866 (mmm) REVERT: O 179 LYS cc_start: 0.6692 (mtmt) cc_final: 0.5974 (tptt) outliers start: 98 outliers final: 73 residues processed: 504 average time/residue: 0.4917 time to fit residues: 399.0815 Evaluate side-chains 503 residues out of total 3498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 416 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 254 VAL 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 136 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 MET 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 167 SER 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 80 ARG 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 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 G residue 249 VAL Chi-restraints excluded: chain G residue 253 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 320 TYR Chi-restraints excluded: chain I residue 328 CYS 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 13 ARG 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 246 ASP 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 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 75 ASP Chi-restraints excluded: chain M residue 133 ILE 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 M residue 341 GLU Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 40 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 131 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 390 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 359 optimal weight: 0.0670 chunk 345 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN B 104 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS ** I 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 HIS ** M 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.159852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118396 restraints weight = 36579.680| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.12 r_work: 0.2989 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.320 32649 Z= 0.212 Angle : 0.759 59.171 44497 Z= 0.435 Chirality : 0.047 0.603 4975 Planarity : 0.004 0.060 5721 Dihedral : 5.149 59.902 4492 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 2.66 % Allowed : 14.19 % Favored : 83.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 4110 helix: 2.31 (0.24), residues: 476 sheet: -0.24 (0.15), residues: 1261 loop : -0.47 (0.13), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 268 HIS 0.008 0.001 HIS K 177 PHE 0.016 0.001 PHE A 13 TYR 0.025 0.002 TYR A 137 ARG 0.006 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 1185) hydrogen bonds : angle 4.95677 ( 3162) SS BOND : bond 0.00361 ( 49) SS BOND : angle 1.19421 ( 98) covalent geometry : bond 0.00512 (32600) covalent geometry : angle 0.75772 (44399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25392.49 seconds wall clock time: 445 minutes 49.07 seconds (26749.07 seconds total)