Starting phenix.real_space_refine on Sun Feb 25 12:15:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff4_29039/02_2024/8ff4_29039_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff4_29039/02_2024/8ff4_29039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff4_29039/02_2024/8ff4_29039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff4_29039/02_2024/8ff4_29039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff4_29039/02_2024/8ff4_29039_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff4_29039/02_2024/8ff4_29039_neut_updated.pdb" } resolution = 3.6 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= 0.113 sd= 0.968 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 859 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 221 5.49 5 Mg 7 5.21 5 S 169 5.16 5 C 31473 2.51 5 N 8660 2.21 5 O 9792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "H TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 251": "OE1" <-> "OE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 194": "OE1" <-> "OE2" Residue "I GLU 235": "OE1" <-> "OE2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "I GLU 446": "OE1" <-> "OE2" Residue "I GLU 468": "OE1" <-> "OE2" Residue "I GLU 471": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L GLU 35": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "P GLU 25": "OE1" <-> "OE2" Residue "P GLU 72": "OE1" <-> "OE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 326": "OE1" <-> "OE2" Residue "Q GLU 10": "OE1" <-> "OE2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q GLU 210": "OE1" <-> "OE2" Residue "Q PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 95": "OE1" <-> "OE2" Residue "R GLU 272": "OE1" <-> "OE2" Residue "R GLU 321": "OE1" <-> "OE2" Residue "S GLU 24": "OE1" <-> "OE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S GLU 76": "OE1" <-> "OE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S GLU 321": "OE1" <-> "OE2" Residue "T GLU 10": "OE1" <-> "OE2" Residue "T GLU 71": "OE1" <-> "OE2" Residue "T GLU 76": "OE1" <-> "OE2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U GLU 38": "OE1" <-> "OE2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U GLU 71": "OE1" <-> "OE2" Residue "U GLU 76": "OE1" <-> "OE2" Residue "U GLU 95": "OE1" <-> "OE2" Residue "U GLU 108": "OE1" <-> "OE2" Residue "U GLU 144": "OE1" <-> "OE2" Residue "U GLU 172": "OE1" <-> "OE2" Residue "U GLU 333": "OE1" <-> "OE2" Residue "V GLU 71": "OE1" <-> "OE2" Residue "V GLU 157": "OE1" <-> "OE2" Residue "V GLU 210": "OE1" <-> "OE2" Residue "V GLU 333": "OE1" <-> "OE2" Residue "W GLU 24": "OE1" <-> "OE2" Residue "W GLU 35": "OE1" <-> "OE2" Residue "W GLU 95": "OE1" <-> "OE2" Residue "W GLU 118": "OE1" <-> "OE2" Residue "W GLU 321": "OE1" <-> "OE2" Residue "W GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50322 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1702 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2330 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "H" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 26, 'rna3p': 36} Chain: "N" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1734 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "O" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1070 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain breaks: 1 Chain: "P" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2618 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain: "Q" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2508 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "R" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "S" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "T" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "U" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "V" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "W" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.33, per 1000 atoms: 0.54 Number of scatterers: 50322 At special positions: 0 Unit cell: (135.966, 238.204, 254.014, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 169 16.00 P 221 15.00 Mg 7 11.99 O 9792 8.00 N 8660 7.00 C 31473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 24.00 Conformation dependent library (CDL) restraints added in 9.1 seconds 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 234 helices and 49 sheets defined 43.7% alpha, 10.4% beta 77 base pairs and 130 stacking pairs defined. Time for finding SS restraints: 24.22 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 84 through 87 No H-bonds generated for 'chain 'B' and resid 84 through 87' Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 186 through 195 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 57 through 70 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 194 through 205 removed outlier: 3.623A pdb=" N ILE C 197 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Proline residue: C 199 - end of helix Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.610A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 57 through 70 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 194 through 205 removed outlier: 3.517A pdb=" N ILE D 197 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 198 " --> pdb=" O SER D 195 " (cutoff:3.500A) Proline residue: D 199 - end of helix Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 292 through 295 Processing helix chain 'D' and resid 302 through 317 Processing helix chain 'E' and resid 57 through 70 Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 194 through 205 Proline residue: E 199 - end of helix Processing helix chain 'E' and resid 256 through 263 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 277 through 284 Processing helix chain 'E' and resid 292 through 295 Processing helix chain 'E' and resid 302 through 317 Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 57 through 70 Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 194 through 205 removed outlier: 3.519A pdb=" N ILE F 197 " --> pdb=" O PHE F 194 " (cutoff:3.500A) Proline residue: F 199 - end of helix Processing helix chain 'F' and resid 257 through 264 Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.642A pdb=" N GLN F 283 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 295 Processing helix chain 'F' and resid 302 through 317 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 57 through 71 Processing helix chain 'G' and resid 99 through 103 Processing helix chain 'G' and resid 194 through 205 Proline residue: G 199 - end of helix Processing helix chain 'G' and resid 256 through 264 Processing helix chain 'G' and resid 269 through 271 No H-bonds generated for 'chain 'G' and resid 269 through 271' Processing helix chain 'G' and resid 277 through 283 Processing helix chain 'G' and resid 292 through 295 Processing helix chain 'G' and resid 302 through 316 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 57 through 70 Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 194 through 205 removed outlier: 3.777A pdb=" N ILE H 197 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) Proline residue: H 199 - end of helix Processing helix chain 'H' and resid 256 through 264 Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'H' and resid 277 through 283 Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 302 through 317 Processing helix chain 'I' and resid 20 through 39 Processing helix chain 'I' and resid 43 through 45 No H-bonds generated for 'chain 'I' and resid 43 through 45' Processing helix chain 'I' and resid 67 through 78 Processing helix chain 'I' and resid 99 through 112 Processing helix chain 'I' and resid 148 through 156 removed outlier: 3.668A pdb=" N PHE I 152 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA I 153 " --> pdb=" O GLN I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 186 No H-bonds generated for 'chain 'I' and resid 184 through 186' Processing helix chain 'I' and resid 196 through 208 Proline residue: I 206 - end of helix Processing helix chain 'I' and resid 239 through 251 removed outlier: 4.042A pdb=" N GLN I 251 " --> pdb=" O TRP I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 257 No H-bonds generated for 'chain 'I' and resid 254 through 257' Processing helix chain 'I' and resid 262 through 269 Processing helix chain 'I' and resid 312 through 324 Processing helix chain 'I' and resid 343 through 354 Processing helix chain 'I' and resid 358 through 360 No H-bonds generated for 'chain 'I' and resid 358 through 360' Processing helix chain 'I' and resid 362 through 366 Processing helix chain 'I' and resid 374 through 392 removed outlier: 3.957A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY I 385 " --> pdb=" O SER I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 420 removed outlier: 3.641A pdb=" N GLN I 398 " --> pdb=" O GLU I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 442 Processing helix chain 'I' and resid 446 through 460 Processing helix chain 'I' and resid 464 through 468 Processing helix chain 'I' and resid 470 through 479 Processing helix chain 'I' and resid 482 through 494 Processing helix chain 'J' and resid 6 through 32 Processing helix chain 'J' and resid 42 through 53 Processing helix chain 'J' and resid 59 through 72 removed outlier: 6.086A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 Processing helix chain 'J' and resid 82 through 90 Processing helix chain 'J' and resid 94 through 107 Processing helix chain 'J' and resid 109 through 111 No H-bonds generated for 'chain 'J' and resid 109 through 111' Processing helix chain 'K' and resid 6 through 32 Processing helix chain 'K' and resid 42 through 53 Processing helix chain 'K' and resid 59 through 72 removed outlier: 6.029A pdb=" N TYR K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 Processing helix chain 'K' and resid 83 through 90 Processing helix chain 'K' and resid 94 through 108 Processing helix chain 'L' and resid 6 through 32 Processing helix chain 'L' and resid 42 through 54 Processing helix chain 'L' and resid 58 through 72 Processing helix chain 'L' and resid 76 through 80 Processing helix chain 'L' and resid 83 through 91 Processing helix chain 'L' and resid 94 through 106 Processing helix chain 'P' and resid 37 through 47 Processing helix chain 'P' and resid 52 through 64 removed outlier: 4.670A pdb=" N ALA P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Proline residue: P 62 - end of helix Processing helix chain 'P' and resid 70 through 75 removed outlier: 4.048A pdb=" N SER P 75 " --> pdb=" O SER P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 82 removed outlier: 3.713A pdb=" N LEU P 82 " --> pdb=" O SER P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 92 Processing helix chain 'P' and resid 96 through 108 Processing helix chain 'P' and resid 114 through 117 Processing helix chain 'P' and resid 120 through 122 No H-bonds generated for 'chain 'P' and resid 120 through 122' Processing helix chain 'P' and resid 140 through 148 Processing helix chain 'P' and resid 157 through 160 Processing helix chain 'P' and resid 215 through 234 removed outlier: 4.557A pdb=" N VAL P 219 " --> pdb=" O GLU P 215 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN P 220 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR P 231 " --> pdb=" O LEU P 227 " (cutoff:3.500A) Proline residue: P 232 - end of helix Processing helix chain 'P' and resid 240 through 260 Processing helix chain 'P' and resid 263 through 280 removed outlier: 4.385A pdb=" N GLY P 269 " --> pdb=" O GLY P 266 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY P 270 " --> pdb=" O ASP P 267 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 271 " --> pdb=" O LEU P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 289 through 299 removed outlier: 4.825A pdb=" N ILE P 294 " --> pdb=" O VAL P 290 " (cutoff:3.500A) Proline residue: P 295 - end of helix Processing helix chain 'P' and resid 304 through 309 Processing helix chain 'P' and resid 312 through 322 Processing helix chain 'Q' and resid 9 through 12 removed outlier: 3.716A pdb=" N LEU Q 12 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 9 through 12' Processing helix chain 'Q' and resid 16 through 25 Processing helix chain 'Q' and resid 31 through 45 Processing helix chain 'Q' and resid 63 through 82 Proline residue: Q 80 - end of helix Processing helix chain 'Q' and resid 106 through 116 Processing helix chain 'Q' and resid 150 through 163 Processing helix chain 'Q' and resid 173 through 177 Processing helix chain 'Q' and resid 182 through 199 removed outlier: 4.237A pdb=" N GLN Q 186 " --> pdb=" O GLY Q 182 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU Q 189 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET Q 198 " --> pdb=" O SER Q 194 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR Q 199 " --> pdb=" O LEU Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 209 through 213 removed outlier: 3.645A pdb=" N THR Q 213 " --> pdb=" O GLU Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 218 through 223 Processing helix chain 'Q' and resid 238 through 253 Processing helix chain 'Q' and resid 265 through 272 removed outlier: 4.661A pdb=" N GLU Q 268 " --> pdb=" O ASP Q 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 278 through 294 Processing helix chain 'Q' and resid 302 through 307 Processing helix chain 'Q' and resid 312 through 330 Processing helix chain 'R' and resid 9 through 12 Processing helix chain 'R' and resid 16 through 25 Processing helix chain 'R' and resid 31 through 45 Processing helix chain 'R' and resid 63 through 84 Proline residue: R 80 - end of helix removed outlier: 3.634A pdb=" N SER R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 117 Processing helix chain 'R' and resid 149 through 163 Processing helix chain 'R' and resid 173 through 177 Processing helix chain 'R' and resid 182 through 199 removed outlier: 3.867A pdb=" N LEU R 185 " --> pdb=" O GLY R 182 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N MET R 198 " --> pdb=" O LEU R 195 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR R 199 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 219 through 223 Processing helix chain 'R' and resid 238 through 253 Processing helix chain 'R' and resid 265 through 274 removed outlier: 4.643A pdb=" N GLU R 268 " --> pdb=" O ASP R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 295 Processing helix chain 'R' and resid 302 through 307 Processing helix chain 'R' and resid 312 through 328 removed outlier: 3.849A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 342 removed outlier: 3.727A pdb=" N ASN R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 13 removed outlier: 3.660A pdb=" N LEU S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 25 Processing helix chain 'S' and resid 31 through 45 Processing helix chain 'S' and resid 63 through 82 Proline residue: S 80 - end of helix Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 149 through 163 Processing helix chain 'S' and resid 173 through 177 Processing helix chain 'S' and resid 182 through 199 removed outlier: 3.919A pdb=" N LEU S 185 " --> pdb=" O GLY S 182 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET S 198 " --> pdb=" O LEU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 209 through 214 Processing helix chain 'S' and resid 219 through 223 Processing helix chain 'S' and resid 238 through 253 Processing helix chain 'S' and resid 265 through 274 removed outlier: 4.666A pdb=" N GLU S 268 " --> pdb=" O ASP S 265 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG S 273 " --> pdb=" O PHE S 270 " (cutoff:3.500A) Processing helix chain 'S' and resid 278 through 294 Processing helix chain 'S' and resid 302 through 308 removed outlier: 3.611A pdb=" N ARG S 308 " --> pdb=" O ASP S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 312 through 328 Processing helix chain 'S' and resid 333 through 343 Processing helix chain 'T' and resid 9 through 12 removed outlier: 3.511A pdb=" N LEU T 12 " --> pdb=" O LEU T 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 9 through 12' Processing helix chain 'T' and resid 16 through 25 Processing helix chain 'T' and resid 31 through 45 Processing helix chain 'T' and resid 63 through 84 Proline residue: T 80 - end of helix removed outlier: 4.017A pdb=" N SER T 84 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 117 Processing helix chain 'T' and resid 149 through 163 Processing helix chain 'T' and resid 173 through 177 Processing helix chain 'T' and resid 182 through 199 removed outlier: 4.003A pdb=" N GLN T 186 " --> pdb=" O GLY T 182 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 209 through 214 removed outlier: 3.508A pdb=" N THR T 213 " --> pdb=" O GLU T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 219 through 224 Processing helix chain 'T' and resid 238 through 253 Processing helix chain 'T' and resid 267 through 274 Processing helix chain 'T' and resid 278 through 295 Processing helix chain 'T' and resid 302 through 307 Processing helix chain 'T' and resid 312 through 328 Processing helix chain 'T' and resid 333 through 343 Processing helix chain 'U' and resid 9 through 12 Processing helix chain 'U' and resid 16 through 25 Processing helix chain 'U' and resid 31 through 45 Processing helix chain 'U' and resid 63 through 84 Proline residue: U 80 - end of helix removed outlier: 3.539A pdb=" N SER U 84 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 117 Processing helix chain 'U' and resid 149 through 163 Processing helix chain 'U' and resid 173 through 177 Processing helix chain 'U' and resid 183 through 199 removed outlier: 4.354A pdb=" N MET U 198 " --> pdb=" O LEU U 195 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR U 199 " --> pdb=" O ALA U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 214 Processing helix chain 'U' and resid 219 through 223 Processing helix chain 'U' and resid 238 through 253 Processing helix chain 'U' and resid 264 through 274 removed outlier: 4.932A pdb=" N GLU U 268 " --> pdb=" O ASP U 265 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR U 269 " --> pdb=" O HIS U 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR U 274 " --> pdb=" O TYR U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 295 Processing helix chain 'U' and resid 302 through 307 Processing helix chain 'U' and resid 312 through 328 Processing helix chain 'U' and resid 333 through 343 Processing helix chain 'V' and resid 9 through 12 Processing helix chain 'V' and resid 16 through 25 Processing helix chain 'V' and resid 31 through 45 Processing helix chain 'V' and resid 63 through 77 Processing helix chain 'V' and resid 79 through 84 Processing helix chain 'V' and resid 106 through 117 Processing helix chain 'V' and resid 149 through 163 Processing helix chain 'V' and resid 173 through 177 Processing helix chain 'V' and resid 184 through 199 removed outlier: 4.014A pdb=" N LEU V 189 " --> pdb=" O LEU V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 209 through 214 Processing helix chain 'V' and resid 218 through 223 Processing helix chain 'V' and resid 238 through 253 Processing helix chain 'V' and resid 265 through 274 removed outlier: 4.737A pdb=" N GLU V 268 " --> pdb=" O ASP V 265 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 294 Processing helix chain 'V' and resid 302 through 308 removed outlier: 3.605A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 328 removed outlier: 3.846A pdb=" N LYS V 317 " --> pdb=" O ALA V 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE V 319 " --> pdb=" O CYS V 315 " (cutoff:3.500A) Processing helix chain 'V' and resid 333 through 343 Processing helix chain 'W' and resid 9 through 11 No H-bonds generated for 'chain 'W' and resid 9 through 11' Processing helix chain 'W' and resid 16 through 25 Processing helix chain 'W' and resid 31 through 45 Processing helix chain 'W' and resid 63 through 84 removed outlier: 3.649A pdb=" N LEU W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) Proline residue: W 80 - end of helix removed outlier: 4.117A pdb=" N SER W 84 " --> pdb=" O PRO W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 117 Processing helix chain 'W' and resid 149 through 163 Processing helix chain 'W' and resid 173 through 176 Processing helix chain 'W' and resid 184 through 199 Processing helix chain 'W' and resid 209 through 214 removed outlier: 3.550A pdb=" N THR W 213 " --> pdb=" O GLU W 210 " (cutoff:3.500A) Processing helix chain 'W' and resid 219 through 223 Processing helix chain 'W' and resid 238 through 253 Processing helix chain 'W' and resid 264 through 274 removed outlier: 4.815A pdb=" N GLU W 268 " --> pdb=" O ASP W 265 " (cutoff:3.500A) Processing helix chain 'W' and resid 278 through 294 Processing helix chain 'W' and resid 302 through 307 removed outlier: 3.627A pdb=" N GLN W 306 " --> pdb=" O LEU W 302 " (cutoff:3.500A) Processing helix chain 'W' and resid 312 through 328 Processing helix chain 'W' and resid 333 through 342 Processing sheet with id= A, first strand: chain 'A' and resid 147 through 150 Processing sheet with id= B, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.984A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.600A pdb=" N ARG A 160 " --> pdb=" O MET A 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 171 through 176 removed outlier: 6.915A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 105 through 108 removed outlier: 4.490A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 18 through 20 Processing sheet with id= G, first strand: chain 'B' and resid 208 through 210 Processing sheet with id= H, first strand: chain 'B' and resid 160 through 165 Processing sheet with id= I, first strand: chain 'C' and resid 297 through 299 removed outlier: 3.665A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= K, first strand: chain 'C' and resid 43 through 45 Processing sheet with id= L, first strand: chain 'C' and resid 77 through 79 Processing sheet with id= M, first strand: chain 'C' and resid 155 through 162 Processing sheet with id= N, first strand: chain 'D' and resid 297 through 299 removed outlier: 3.610A pdb=" N GLY D 276 " --> pdb=" O TYR D 299 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 225 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 25 through 27 Processing sheet with id= P, first strand: chain 'D' and resid 43 through 45 Processing sheet with id= Q, first strand: chain 'D' and resid 77 through 79 Processing sheet with id= R, first strand: chain 'E' and resid 297 through 299 removed outlier: 3.546A pdb=" N GLY E 276 " --> pdb=" O TYR E 299 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER E 225 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 25 through 27 Processing sheet with id= T, first strand: chain 'E' and resid 77 through 79 Processing sheet with id= U, first strand: chain 'E' and resid 155 through 159 Processing sheet with id= V, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.565A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 140 through 142 removed outlier: 3.604A pdb=" N TYR F 182 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 225 " --> pdb=" O LEU F 21 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS F 297 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLY F 276 " --> pdb=" O HIS F 297 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR F 299 " --> pdb=" O GLY F 276 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 43 through 45 Processing sheet with id= Y, first strand: chain 'F' and resid 77 through 79 Processing sheet with id= Z, first strand: chain 'F' and resid 155 through 158 Processing sheet with id= AA, first strand: chain 'G' and resid 145 through 147 removed outlier: 4.656A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 225 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS G 297 " --> pdb=" O ILE G 274 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLY G 276 " --> pdb=" O HIS G 297 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR G 299 " --> pdb=" O GLY G 276 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.782A pdb=" N GLY G 25 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 43 through 45 Processing sheet with id= AD, first strand: chain 'G' and resid 77 through 80 Processing sheet with id= AE, first strand: chain 'G' and resid 155 through 159 Processing sheet with id= AF, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.309A pdb=" N HIS H 297 " --> pdb=" O ILE H 274 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY H 276 " --> pdb=" O HIS H 297 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR H 299 " --> pdb=" O GLY H 276 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 24 through 27 Processing sheet with id= AH, first strand: chain 'H' and resid 43 through 45 Processing sheet with id= AI, first strand: chain 'H' and resid 77 through 80 Processing sheet with id= AJ, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.081A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 61 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 11 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= AL, first strand: chain 'I' and resid 125 through 132 Processing sheet with id= AM, first strand: chain 'I' and resid 210 through 214 removed outlier: 4.485A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 120 through 122 Processing sheet with id= AO, first strand: chain 'Q' and resid 55 through 57 removed outlier: 7.220A pdb=" N ILE Q 228 " --> pdb=" O TYR Q 56 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'Q' and resid 91 through 95 removed outlier: 6.175A pdb=" N VAL Q 167 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE Q 94 " --> pdb=" O VAL Q 167 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE Q 169 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU Q 202 " --> pdb=" O PHE Q 168 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL Q 170 " --> pdb=" O LEU Q 202 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N CYS Q 204 " --> pdb=" O VAL Q 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'R' and resid 225 through 230 removed outlier: 6.260A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE R 230 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR R 56 " --> pdb=" O PHE R 230 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS R 203 " --> pdb=" O ILE R 53 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL R 55 " --> pdb=" O HIS R 203 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU R 205 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLY R 57 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLY R 207 " --> pdb=" O GLY R 57 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE R 168 " --> pdb=" O CYS R 204 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU R 206 " --> pdb=" O PHE R 168 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL R 170 " --> pdb=" O LEU R 206 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL R 92 " --> pdb=" O VAL R 167 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'S' and resid 225 through 230 removed outlier: 6.879A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE S 230 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR S 56 " --> pdb=" O PHE S 230 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS S 203 " --> pdb=" O ILE S 53 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL S 55 " --> pdb=" O HIS S 203 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU S 205 " --> pdb=" O VAL S 55 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLY S 57 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLY S 207 " --> pdb=" O GLY S 57 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'T' and resid 225 through 230 removed outlier: 6.792A pdb=" N PHE T 52 " --> pdb=" O VAL T 226 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR T 56 " --> pdb=" O PHE T 230 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS T 203 " --> pdb=" O ILE T 53 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL T 55 " --> pdb=" O HIS T 203 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU T 205 " --> pdb=" O VAL T 55 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY T 57 " --> pdb=" O LEU T 205 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'U' and resid 225 through 230 removed outlier: 6.809A pdb=" N PHE U 52 " --> pdb=" O VAL U 226 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE U 228 " --> pdb=" O PHE U 52 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE U 54 " --> pdb=" O ILE U 228 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE U 230 " --> pdb=" O PHE U 54 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR U 56 " --> pdb=" O PHE U 230 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS U 203 " --> pdb=" O ILE U 53 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL U 55 " --> pdb=" O HIS U 203 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU U 205 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLY U 57 " --> pdb=" O LEU U 205 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE U 168 " --> pdb=" O CYS U 204 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU U 206 " --> pdb=" O PHE U 168 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL U 170 " --> pdb=" O LEU U 206 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'V' and resid 225 through 230 removed outlier: 6.703A pdb=" N PHE V 52 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE V 228 " --> pdb=" O PHE V 52 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE V 54 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE V 230 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR V 56 " --> pdb=" O PHE V 230 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS V 203 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL V 55 " --> pdb=" O HIS V 203 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU V 205 " --> pdb=" O VAL V 55 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLY V 57 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLY V 207 " --> pdb=" O GLY V 57 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE V 168 " --> pdb=" O CYS V 204 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU V 206 " --> pdb=" O PHE V 168 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL V 170 " --> pdb=" O LEU V 206 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL V 92 " --> pdb=" O PHE V 169 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASP V 171 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE V 94 " --> pdb=" O ASP V 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'W' and resid 225 through 229 removed outlier: 6.685A pdb=" N PHE W 52 " --> pdb=" O VAL W 226 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE W 228 " --> pdb=" O PHE W 52 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE W 54 " --> pdb=" O ILE W 228 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N HIS W 203 " --> pdb=" O ILE W 53 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL W 55 " --> pdb=" O HIS W 203 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU W 205 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL W 92 " --> pdb=" O PHE W 169 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'W' and resid 133 through 135 1820 hydrogen bonds defined for protein. 4740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 187 hydrogen bonds 374 hydrogen bond angles 0 basepair planarities 77 basepair parallelities 130 stacking parallelities Total time for adding SS restraints: 20.33 Time building geometry restraints manager: 25.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 15392 1.34 - 1.46: 13510 1.46 - 1.59: 22312 1.59 - 1.71: 409 1.71 - 1.84: 253 Bond restraints: 51876 Sorted by residual: bond pdb=" N SER V 59 " pdb=" CA SER V 59 " ideal model delta sigma weight residual 1.463 1.433 0.030 1.30e-02 5.92e+03 5.23e+00 bond pdb=" CA VAL T 61 " pdb=" C VAL T 61 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.27e-02 6.20e+03 3.82e+00 bond pdb=" CA ASP D 246 " pdb=" C ASP D 246 " ideal model delta sigma weight residual 1.524 1.508 0.016 8.10e-03 1.52e+04 3.68e+00 bond pdb=" CA SER U 59 " pdb=" C SER U 59 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.30e-02 5.92e+03 3.49e+00 bond pdb=" O3' DC N 50 " pdb=" P DT N 51 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.50e-02 4.44e+03 3.34e+00 ... (remaining 51871 not shown) Histogram of bond angle deviations from ideal: 94.92 - 103.90: 1139 103.90 - 112.89: 28170 112.89 - 121.88: 31033 121.88 - 130.87: 10410 130.87 - 139.86: 303 Bond angle restraints: 71055 Sorted by residual: angle pdb=" N THR U 299 " pdb=" CA THR U 299 " pdb=" C THR U 299 " ideal model delta sigma weight residual 108.74 115.59 -6.85 1.38e+00 5.25e-01 2.46e+01 angle pdb=" N ALA U 58 " pdb=" CA ALA U 58 " pdb=" C ALA U 58 " ideal model delta sigma weight residual 110.41 116.25 -5.84 1.23e+00 6.61e-01 2.26e+01 angle pdb=" C VAL R 61 " pdb=" N GLY R 62 " pdb=" CA GLY R 62 " ideal model delta sigma weight residual 122.26 116.33 5.93 1.34e+00 5.57e-01 1.96e+01 angle pdb=" N TYR K 108 " pdb=" CA TYR K 108 " pdb=" C TYR K 108 " ideal model delta sigma weight residual 112.90 107.11 5.79 1.31e+00 5.83e-01 1.96e+01 angle pdb=" C TYR I 40 " pdb=" N PRO I 41 " pdb=" CA PRO I 41 " ideal model delta sigma weight residual 119.19 114.59 4.60 1.06e+00 8.90e-01 1.89e+01 ... (remaining 71050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 29243 35.81 - 71.62: 1614 71.62 - 107.43: 86 107.43 - 143.24: 3 143.24 - 179.05: 6 Dihedral angle restraints: 30952 sinusoidal: 14414 harmonic: 16538 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 20.95 179.05 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 52.72 147.28 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual 232.00 66.54 165.46 1 1.70e+01 3.46e-03 6.54e+01 ... (remaining 30949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 6246 0.045 - 0.091: 1165 0.091 - 0.136: 335 0.136 - 0.182: 27 0.182 - 0.227: 6 Chirality restraints: 7779 Sorted by residual: chirality pdb=" C3' A M 38 " pdb=" C4' A M 38 " pdb=" O3' A M 38 " pdb=" C2' A M 38 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE J 13 " pdb=" CA ILE J 13 " pdb=" CG1 ILE J 13 " pdb=" CG2 ILE J 13 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE H 267 " pdb=" CA ILE H 267 " pdb=" CG1 ILE H 267 " pdb=" CG2 ILE H 267 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 7776 not shown) Planarity restraints: 8346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO F 247 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C PHE J 61 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 61 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C PHE K 61 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE K 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS K 62 " -0.018 2.00e-02 2.50e+03 ... (remaining 8343 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 579 2.57 - 3.15: 42389 3.15 - 3.73: 85369 3.73 - 4.32: 116776 4.32 - 4.90: 186623 Nonbonded interactions: 431736 Sorted by model distance: nonbonded pdb=" O3A ATP V 600 " pdb="MG MG V 601 " model vdw 1.983 2.170 nonbonded pdb=" O3B ATP T 600 " pdb="MG MG T 601 " model vdw 1.995 2.170 nonbonded pdb=" O3B ATP U 600 " pdb="MG MG U 601 " model vdw 2.000 2.170 nonbonded pdb=" O3B ATP Q 600 " pdb="MG MG Q 601 " model vdw 2.003 2.170 nonbonded pdb=" O3B ATP S 600 " pdb="MG MG S 601 " model vdw 2.005 2.170 ... (remaining 431731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'Q' selection = (chain 'R' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'S' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'T' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'U' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'V' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) selection = (chain 'W' and (resid 4 through 129 or resid 149 through 332 or resid 600 throug \ h 601)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.050 Extract box with map and model: 14.660 Check model and map are aligned: 0.730 Set scattering table: 0.440 Process input model: 154.420 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.300 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 51876 Z= 0.188 Angle : 0.643 10.058 71055 Z= 0.364 Chirality : 0.040 0.227 7779 Planarity : 0.004 0.088 8346 Dihedral : 19.458 179.052 20314 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.84 % Favored : 93.60 % Rotamer: Outliers : 0.71 % Allowed : 22.68 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: 0.08 (0.12), residues: 5598 helix: 1.17 (0.10), residues: 2570 sheet: -0.83 (0.18), residues: 800 loop : -0.86 (0.14), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP I 63 HIS 0.010 0.001 HIS W 162 PHE 0.047 0.001 PHE V 126 TYR 0.038 0.001 TYR C 244 ARG 0.011 0.000 ARG V 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 422 time to evaluate : 6.294 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 1 MET cc_start: 0.6465 (tpt) cc_final: 0.6155 (tpt) REVERT: A 116 LEU cc_start: 0.9228 (tp) cc_final: 0.8950 (tp) REVERT: A 209 GLN cc_start: 0.8860 (tt0) cc_final: 0.8573 (mt0) REVERT: B 118 ARG cc_start: 0.5287 (tmt170) cc_final: 0.4274 (ttt-90) REVERT: B 213 ARG cc_start: 0.4531 (tpp80) cc_final: 0.4012 (tpp80) REVERT: F 260 ASP cc_start: 0.9111 (t0) cc_final: 0.8903 (t0) REVERT: I 46 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7276 (mtt180) REVERT: I 358 TRP cc_start: 0.5740 (OUTLIER) cc_final: 0.5476 (p90) REVERT: J 87 LEU cc_start: 0.9249 (tp) cc_final: 0.9004 (tp) REVERT: P 40 TYR cc_start: 0.9251 (t80) cc_final: 0.8862 (t80) REVERT: P 99 GLU cc_start: 0.9395 (tp30) cc_final: 0.9156 (tp30) REVERT: P 272 MET cc_start: 0.8879 (ttm) cc_final: 0.8507 (ttm) REVERT: Q 191 CYS cc_start: 0.8268 (m) cc_final: 0.7975 (t) REVERT: S 9 LEU cc_start: 0.8215 (pt) cc_final: 0.7954 (mp) REVERT: T 61 VAL cc_start: 0.7330 (OUTLIER) cc_final: 0.6995 (m) REVERT: U 24 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7866 (mt-10) REVERT: U 86 ARG cc_start: 0.8396 (mmm160) cc_final: 0.7913 (mmm160) REVERT: W 61 VAL cc_start: 0.5589 (OUTLIER) cc_final: 0.5383 (m) REVERT: W 97 ILE cc_start: 0.7842 (pt) cc_final: 0.7549 (tt) REVERT: W 201 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7758 (mm) outliers start: 35 outliers final: 9 residues processed: 447 average time/residue: 0.6258 time to fit residues: 471.6612 Evaluate side-chains 384 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 370 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain I residue 46 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 291 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 485 optimal weight: 0.4980 chunk 435 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 450 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 chunk 522 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 124 HIS ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 216 ASN T 25 ASN ** T 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 51876 Z= 0.316 Angle : 0.607 11.015 71055 Z= 0.321 Chirality : 0.041 0.210 7779 Planarity : 0.005 0.090 8346 Dihedral : 18.388 175.682 9002 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.75 % Favored : 93.80 % Rotamer: Outliers : 3.16 % Allowed : 20.40 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: 0.05 (0.12), residues: 5598 helix: 1.10 (0.10), residues: 2600 sheet: -0.89 (0.18), residues: 789 loop : -0.83 (0.14), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 52 HIS 0.006 0.001 HIS G 171 PHE 0.023 0.002 PHE I 362 TYR 0.019 0.002 TYR D 183 ARG 0.006 0.000 ARG I 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 373 time to evaluate : 5.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8210 (p0) cc_final: 0.7850 (p0) REVERT: A 209 GLN cc_start: 0.8954 (tt0) cc_final: 0.8598 (mt0) REVERT: D 226 LEU cc_start: 0.9090 (mt) cc_final: 0.8780 (mt) REVERT: E 77 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8640 (ttp-170) REVERT: F 30 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7979 (m110) REVERT: F 77 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8859 (ttp-170) REVERT: F 137 MET cc_start: 0.8345 (tpp) cc_final: 0.8054 (tpp) REVERT: F 205 MET cc_start: 0.8804 (mmm) cc_final: 0.8554 (mmp) REVERT: F 260 ASP cc_start: 0.9185 (t0) cc_final: 0.8969 (t0) REVERT: G 77 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8069 (mtm-85) REVERT: G 108 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8773 (tp) REVERT: H 250 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7336 (ptmt) REVERT: I 62 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7130 (m-10) REVERT: I 152 PHE cc_start: 0.8333 (t80) cc_final: 0.8115 (t80) REVERT: I 303 MET cc_start: 0.8620 (mmp) cc_final: 0.7995 (mmm) REVERT: I 358 TRP cc_start: 0.5805 (OUTLIER) cc_final: 0.5385 (p90) REVERT: I 451 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8649 (tp30) REVERT: J 63 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7882 (mp0) REVERT: P 40 TYR cc_start: 0.9313 (t80) cc_final: 0.8933 (t80) REVERT: P 267 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8276 (t0) REVERT: Q 215 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.5555 (ptt90) REVERT: R 12 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8516 (mm) REVERT: S 9 LEU cc_start: 0.8291 (pt) cc_final: 0.8069 (mp) REVERT: S 102 ARG cc_start: 0.8448 (ttm110) cc_final: 0.7738 (ttm110) REVERT: S 324 GLU cc_start: 0.8107 (pp20) cc_final: 0.7668 (tm-30) REVERT: T 46 GLU cc_start: 0.8673 (tp30) cc_final: 0.8326 (mm-30) REVERT: T 61 VAL cc_start: 0.7540 (OUTLIER) cc_final: 0.7093 (m) REVERT: V 131 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7952 (mmm160) REVERT: W 273 ARG cc_start: 0.7580 (mmt180) cc_final: 0.7332 (mmt180) outliers start: 157 outliers final: 69 residues processed: 503 average time/residue: 0.6088 time to fit residues: 516.0991 Evaluate side-chains 418 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 336 time to evaluate : 6.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 267 ASP Chi-restraints excluded: chain P residue 282 ASN Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 320 LYS Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 314 GLN Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 318 MET Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 176 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 290 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 434 optimal weight: 4.9990 chunk 355 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 523 optimal weight: 7.9990 chunk 565 optimal weight: 10.0000 chunk 465 optimal weight: 4.9990 chunk 518 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 419 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 166 ASN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN S 124 HIS ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 216 ASN T 197 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 164 HIS ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 197 ASN V 314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 51876 Z= 0.403 Angle : 0.635 10.100 71055 Z= 0.335 Chirality : 0.042 0.202 7779 Planarity : 0.005 0.094 8346 Dihedral : 18.301 174.870 8987 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.36 % Favored : 93.21 % Rotamer: Outliers : 4.15 % Allowed : 20.30 % Favored : 75.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.47 % 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: -0.13 (0.12), residues: 5598 helix: 0.98 (0.10), residues: 2625 sheet: -0.98 (0.19), residues: 771 loop : -0.96 (0.14), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP I 52 HIS 0.008 0.001 HIS B 51 PHE 0.031 0.002 PHE G 234 TYR 0.022 0.002 TYR K 11 ARG 0.005 0.001 ARG I 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 365 time to evaluate : 5.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8412 (p0) cc_final: 0.8059 (p0) REVERT: B 166 ASN cc_start: 0.8891 (m-40) cc_final: 0.8598 (p0) REVERT: C 244 TYR cc_start: 0.7373 (t80) cc_final: 0.6824 (t80) REVERT: E 77 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8678 (ttp-170) REVERT: F 77 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8765 (ttp-170) REVERT: F 205 MET cc_start: 0.8954 (mmm) cc_final: 0.8733 (mmp) REVERT: F 260 ASP cc_start: 0.9227 (t0) cc_final: 0.9019 (t0) REVERT: G 77 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8091 (mtm-85) REVERT: G 229 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: H 216 ILE cc_start: 0.9247 (mm) cc_final: 0.9029 (mm) REVERT: I 62 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: I 152 PHE cc_start: 0.8515 (t80) cc_final: 0.8253 (t80) REVERT: I 358 TRP cc_start: 0.5913 (OUTLIER) cc_final: 0.5694 (p90) REVERT: I 361 ASN cc_start: 0.6108 (OUTLIER) cc_final: 0.5309 (t0) REVERT: I 396 ASP cc_start: 0.7641 (t0) cc_final: 0.7121 (t70) REVERT: I 451 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8521 (tp30) REVERT: J 48 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9452 (tp) REVERT: P 267 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8349 (t0) REVERT: Q 215 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5739 (ptt90) REVERT: R 197 ASN cc_start: 0.8213 (t0) cc_final: 0.7904 (m-40) REVERT: S 74 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7766 (mm) REVERT: S 102 ARG cc_start: 0.8471 (ttm110) cc_final: 0.7967 (ttm110) REVERT: S 126 PHE cc_start: 0.8016 (t80) cc_final: 0.7768 (t80) REVERT: S 324 GLU cc_start: 0.8085 (pp20) cc_final: 0.7574 (tm-30) REVERT: U 95 GLU cc_start: 0.8275 (pm20) cc_final: 0.7306 (pm20) REVERT: U 112 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8339 (mmt-90) REVERT: V 131 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7991 (mmm160) REVERT: V 198 MET cc_start: 0.7878 (mtp) cc_final: 0.7185 (mtt) REVERT: W 285 LEU cc_start: 0.7773 (mt) cc_final: 0.7525 (tt) outliers start: 206 outliers final: 115 residues processed: 536 average time/residue: 0.6228 time to fit residues: 564.3228 Evaluate side-chains 458 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 330 time to evaluate : 6.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 267 ASP Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 282 ASN Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 303 LYS Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 234 CYS Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 133 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 516 optimal weight: 0.9990 chunk 393 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 351 optimal weight: 0.6980 chunk 524 optimal weight: 4.9990 chunk 555 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 497 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN K 25 ASN ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 266 HIS V 197 ASN V 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 51876 Z= 0.266 Angle : 0.570 10.093 71055 Z= 0.300 Chirality : 0.040 0.196 7779 Planarity : 0.004 0.097 8346 Dihedral : 18.152 175.658 8985 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.04 % Favored : 93.53 % Rotamer: Outliers : 3.89 % Allowed : 21.00 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: 0.01 (0.12), residues: 5598 helix: 1.09 (0.10), residues: 2614 sheet: -0.96 (0.19), residues: 778 loop : -0.87 (0.14), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 63 HIS 0.006 0.001 HIS H 171 PHE 0.036 0.001 PHE V 126 TYR 0.024 0.001 TYR W 109 ARG 0.006 0.000 ARG W 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 369 time to evaluate : 6.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6627 (tpt) cc_final: 0.6058 (tpt) REVERT: A 116 LEU cc_start: 0.9305 (tp) cc_final: 0.9098 (tp) REVERT: A 146 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8219 (tttp) REVERT: A 202 ASP cc_start: 0.8444 (p0) cc_final: 0.8078 (p0) REVERT: B 118 ARG cc_start: 0.4428 (tmt170) cc_final: 0.3286 (mtp180) REVERT: B 187 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7540 (tm-30) REVERT: C 244 TYR cc_start: 0.7308 (t80) cc_final: 0.6909 (t80) REVERT: E 77 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8669 (ttp-170) REVERT: E 247 PRO cc_start: 0.7714 (Cg_exo) cc_final: 0.7502 (Cg_endo) REVERT: F 77 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8737 (ttp-170) REVERT: F 260 ASP cc_start: 0.9134 (t0) cc_final: 0.8898 (t0) REVERT: F 280 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8630 (ttpp) REVERT: G 77 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8112 (mtm-85) REVERT: G 108 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8598 (tp) REVERT: I 26 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (mmm) REVERT: I 62 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: I 152 PHE cc_start: 0.8450 (t80) cc_final: 0.8205 (t80) REVERT: I 358 TRP cc_start: 0.5745 (OUTLIER) cc_final: 0.5514 (p90) REVERT: I 361 ASN cc_start: 0.5904 (OUTLIER) cc_final: 0.5183 (t0) REVERT: I 396 ASP cc_start: 0.7563 (t0) cc_final: 0.7349 (t70) REVERT: J 112 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.4613 (p0) REVERT: L 95 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8796 (mp10) REVERT: P 40 TYR cc_start: 0.9358 (t80) cc_final: 0.8900 (t80) REVERT: P 113 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8229 (p0) REVERT: P 267 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8439 (t0) REVERT: Q 100 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8152 (pt0) REVERT: Q 215 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.5754 (ptt90) REVERT: R 12 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8529 (mm) REVERT: R 197 ASN cc_start: 0.8183 (t0) cc_final: 0.7877 (m-40) REVERT: R 198 MET cc_start: 0.9117 (mtm) cc_final: 0.8691 (mtm) REVERT: S 74 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7695 (mm) REVERT: S 102 ARG cc_start: 0.8491 (ttm110) cc_final: 0.7998 (ttm110) REVERT: S 126 PHE cc_start: 0.8083 (t80) cc_final: 0.7554 (t80) REVERT: S 324 GLU cc_start: 0.8058 (pp20) cc_final: 0.7611 (tm-30) REVERT: U 95 GLU cc_start: 0.8292 (pm20) cc_final: 0.7339 (pm20) REVERT: V 24 GLU cc_start: 0.9228 (tp30) cc_final: 0.9026 (tp30) REVERT: V 131 ARG cc_start: 0.8349 (mmm160) cc_final: 0.8083 (mmm160) REVERT: V 198 MET cc_start: 0.7959 (mtp) cc_final: 0.7456 (mtt) REVERT: V 234 CYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7763 (t) REVERT: W 142 ASN cc_start: 0.8120 (t0) cc_final: 0.7889 (p0) REVERT: W 267 TRP cc_start: 0.8884 (p-90) cc_final: 0.8652 (p-90) outliers start: 193 outliers final: 120 residues processed: 529 average time/residue: 0.5972 time to fit residues: 532.7681 Evaluate side-chains 474 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 335 time to evaluate : 5.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 267 ASP Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 55 VAL Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 462 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 413 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 474 optimal weight: 9.9990 chunk 384 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 498 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS S 25 ASN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 51876 Z= 0.254 Angle : 0.560 9.706 71055 Z= 0.294 Chirality : 0.039 0.199 7779 Planarity : 0.004 0.098 8346 Dihedral : 18.055 176.254 8985 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.97 % Favored : 93.62 % Rotamer: Outliers : 4.27 % Allowed : 20.72 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: 0.08 (0.12), residues: 5598 helix: 1.12 (0.10), residues: 2633 sheet: -0.89 (0.19), residues: 765 loop : -0.83 (0.14), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 63 HIS 0.016 0.001 HIS B 51 PHE 0.022 0.001 PHE V 126 TYR 0.020 0.001 TYR P 154 ARG 0.005 0.000 ARG W 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 363 time to evaluate : 5.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.9436 (tmm) cc_final: 0.9156 (tmm) REVERT: A 202 ASP cc_start: 0.8467 (p0) cc_final: 0.8109 (p0) REVERT: B 118 ARG cc_start: 0.4350 (tmt170) cc_final: 0.3224 (mtp180) REVERT: B 187 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7553 (tm-30) REVERT: C 244 TYR cc_start: 0.7322 (t80) cc_final: 0.6884 (t80) REVERT: E 77 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8700 (ttp-170) REVERT: F 77 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8719 (ttp-170) REVERT: F 137 MET cc_start: 0.8266 (tpp) cc_final: 0.7883 (tpt) REVERT: F 260 ASP cc_start: 0.9107 (t0) cc_final: 0.8857 (t0) REVERT: G 77 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8128 (mtm-85) REVERT: G 108 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8544 (tp) REVERT: G 221 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8224 (t80) REVERT: G 229 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: H 250 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7501 (ptmt) REVERT: I 26 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8600 (mmm) REVERT: I 62 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: I 152 PHE cc_start: 0.8476 (t80) cc_final: 0.8226 (t80) REVERT: I 222 LYS cc_start: 0.8003 (tptp) cc_final: 0.7714 (mmmt) REVERT: I 358 TRP cc_start: 0.5963 (OUTLIER) cc_final: 0.5754 (p90) REVERT: I 361 ASN cc_start: 0.5860 (OUTLIER) cc_final: 0.5038 (t0) REVERT: I 396 ASP cc_start: 0.7639 (t0) cc_final: 0.7422 (t70) REVERT: L 95 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: P 40 TYR cc_start: 0.9366 (t80) cc_final: 0.8927 (t80) REVERT: P 113 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8220 (p0) REVERT: P 267 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8455 (t0) REVERT: Q 215 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.5839 (ptt90) REVERT: Q 286 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7983 (ttmm) REVERT: R 197 ASN cc_start: 0.8167 (t0) cc_final: 0.7871 (m-40) REVERT: R 198 MET cc_start: 0.9064 (mtm) cc_final: 0.8265 (mpp) REVERT: S 102 ARG cc_start: 0.8501 (ttm110) cc_final: 0.8009 (ttm110) REVERT: S 126 PHE cc_start: 0.8024 (t80) cc_final: 0.7531 (t80) REVERT: S 251 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7695 (t80) REVERT: S 324 GLU cc_start: 0.7997 (pp20) cc_final: 0.7685 (tm-30) REVERT: U 95 GLU cc_start: 0.8353 (pm20) cc_final: 0.7335 (pm20) REVERT: U 112 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8342 (mmt-90) REVERT: V 102 ARG cc_start: 0.8121 (tmm160) cc_final: 0.7614 (tmm160) REVERT: V 198 MET cc_start: 0.8060 (mtp) cc_final: 0.7189 (mtt) REVERT: V 234 CYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7717 (t) REVERT: W 142 ASN cc_start: 0.8245 (t0) cc_final: 0.7894 (p0) REVERT: W 198 MET cc_start: 0.7996 (mmm) cc_final: 0.7502 (mpp) REVERT: W 267 TRP cc_start: 0.8941 (p-90) cc_final: 0.8690 (p-90) outliers start: 212 outliers final: 126 residues processed: 539 average time/residue: 0.6064 time to fit residues: 551.9565 Evaluate side-chains 483 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 338 time to evaluate : 6.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 267 ASP Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 286 LYS Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain Q residue 303 LYS Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 301 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 186 optimal weight: 0.5980 chunk 500 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 326 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 556 optimal weight: 9.9990 chunk 461 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 292 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS S 25 ASN ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 197 ASN T 203 HIS ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 158 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 51876 Z= 0.327 Angle : 0.593 15.896 71055 Z= 0.309 Chirality : 0.040 0.240 7779 Planarity : 0.004 0.150 8346 Dihedral : 18.034 175.671 8982 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.23 % Favored : 93.34 % Rotamer: Outliers : 4.17 % Allowed : 21.08 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: 0.04 (0.12), residues: 5598 helix: 1.10 (0.10), residues: 2628 sheet: -0.95 (0.19), residues: 787 loop : -0.83 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 63 HIS 0.017 0.001 HIS B 51 PHE 0.027 0.001 PHE G 234 TYR 0.029 0.001 TYR A 37 ARG 0.006 0.000 ARG I 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 353 time to evaluate : 5.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8497 (p0) cc_final: 0.8176 (p0) REVERT: B 118 ARG cc_start: 0.4458 (tmt170) cc_final: 0.3479 (mmm-85) REVERT: B 187 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7619 (tm-30) REVERT: C 244 TYR cc_start: 0.7472 (t80) cc_final: 0.7000 (t80) REVERT: D 77 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8380 (ttp80) REVERT: E 77 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8673 (ttp-170) REVERT: F 77 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.9009 (mtm110) REVERT: F 137 MET cc_start: 0.8263 (tpp) cc_final: 0.7855 (tpt) REVERT: F 142 MET cc_start: 0.8735 (tpp) cc_final: 0.8505 (tpp) REVERT: F 260 ASP cc_start: 0.9140 (t0) cc_final: 0.8893 (t0) REVERT: G 77 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8116 (mtm-85) REVERT: G 108 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8540 (tp) REVERT: I 26 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8666 (mmm) REVERT: I 358 TRP cc_start: 0.6057 (OUTLIER) cc_final: 0.5574 (p90) REVERT: I 361 ASN cc_start: 0.6060 (OUTLIER) cc_final: 0.5292 (t0) REVERT: I 396 ASP cc_start: 0.7745 (t0) cc_final: 0.7525 (t70) REVERT: J 112 ASP cc_start: 0.5712 (OUTLIER) cc_final: 0.4563 (p0) REVERT: L 95 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8735 (mp10) REVERT: P 113 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8251 (p0) REVERT: P 171 LYS cc_start: 0.9360 (mttt) cc_final: 0.8919 (tttt) REVERT: Q 100 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: Q 215 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.5911 (ptt90) REVERT: R 197 ASN cc_start: 0.8178 (t0) cc_final: 0.7895 (m-40) REVERT: R 198 MET cc_start: 0.9044 (mtm) cc_final: 0.8196 (mpp) REVERT: R 321 GLU cc_start: 0.8573 (tt0) cc_final: 0.8165 (tm-30) REVERT: S 74 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7762 (mm) REVERT: S 102 ARG cc_start: 0.8506 (ttm110) cc_final: 0.8027 (ttm110) REVERT: S 126 PHE cc_start: 0.8088 (t80) cc_final: 0.7816 (t80) REVERT: S 324 GLU cc_start: 0.8040 (pp20) cc_final: 0.7736 (tm-30) REVERT: U 24 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8431 (tm-30) REVERT: U 95 GLU cc_start: 0.8336 (pm20) cc_final: 0.7552 (pm20) REVERT: U 112 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8331 (mmt-90) REVERT: V 128 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: V 145 SER cc_start: 0.9482 (m) cc_final: 0.9065 (t) REVERT: V 164 HIS cc_start: 0.8799 (t-90) cc_final: 0.8579 (t70) REVERT: W 142 ASN cc_start: 0.8313 (t0) cc_final: 0.7904 (p0) REVERT: W 267 TRP cc_start: 0.9012 (p-90) cc_final: 0.8689 (p-90) outliers start: 207 outliers final: 145 residues processed: 531 average time/residue: 0.6025 time to fit residues: 536.8170 Evaluate side-chains 492 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 331 time to evaluate : 5.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 267 ASP Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 215 ARG Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain Q residue 303 LYS Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 301 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 536 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 316 optimal weight: 9.9990 chunk 406 optimal weight: 1.9990 chunk 314 optimal weight: 0.9980 chunk 468 optimal weight: 10.0000 chunk 310 optimal weight: 0.5980 chunk 554 optimal weight: 0.3980 chunk 346 optimal weight: 10.0000 chunk 337 optimal weight: 0.9990 chunk 255 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 HIS ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN H 13 ASN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 203 HIS R 137 ASN S 25 ASN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN U 142 ASN V 316 GLN W 158 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 51876 Z= 0.166 Angle : 0.540 11.139 71055 Z= 0.282 Chirality : 0.038 0.198 7779 Planarity : 0.004 0.126 8346 Dihedral : 17.915 175.500 8982 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.57 % Favored : 94.03 % Rotamer: Outliers : 2.96 % Allowed : 22.21 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: 0.22 (0.12), residues: 5598 helix: 1.22 (0.11), residues: 2606 sheet: -0.88 (0.19), residues: 793 loop : -0.68 (0.14), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP I 73 HIS 0.017 0.001 HIS B 51 PHE 0.028 0.001 PHE G 234 TYR 0.028 0.001 TYR A 37 ARG 0.009 0.000 ARG W 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 374 time to evaluate : 5.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6859 (tpt) cc_final: 0.6389 (tpt) REVERT: A 39 MET cc_start: 0.9405 (tmm) cc_final: 0.9125 (tmm) REVERT: A 202 ASP cc_start: 0.8498 (p0) cc_final: 0.8166 (p0) REVERT: A 209 GLN cc_start: 0.9006 (mt0) cc_final: 0.8609 (mt0) REVERT: B 118 ARG cc_start: 0.4154 (tmt170) cc_final: 0.3095 (mtp180) REVERT: B 187 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7548 (tm-30) REVERT: C 244 TYR cc_start: 0.7339 (t80) cc_final: 0.6932 (t80) REVERT: D 77 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8256 (ttp80) REVERT: E 77 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8739 (ttp-170) REVERT: F 77 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8674 (ttp-170) REVERT: F 142 MET cc_start: 0.8741 (tpp) cc_final: 0.8488 (tpp) REVERT: F 260 ASP cc_start: 0.9053 (t0) cc_final: 0.8830 (t0) REVERT: F 268 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8732 (p0) REVERT: G 77 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8071 (mtm-85) REVERT: G 221 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.8172 (t80) REVERT: H 251 GLU cc_start: 0.8132 (mp0) cc_final: 0.7559 (mp0) REVERT: H 302 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8658 (mtt90) REVERT: I 26 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8453 (mmm) REVERT: I 222 LYS cc_start: 0.8000 (tptp) cc_final: 0.7726 (mmmt) REVERT: I 358 TRP cc_start: 0.5909 (OUTLIER) cc_final: 0.5448 (p90) REVERT: I 396 ASP cc_start: 0.7601 (t0) cc_final: 0.7360 (t70) REVERT: J 112 ASP cc_start: 0.5822 (OUTLIER) cc_final: 0.4665 (p0) REVERT: L 95 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8748 (mp10) REVERT: P 40 TYR cc_start: 0.9356 (t80) cc_final: 0.8882 (t80) REVERT: P 171 LYS cc_start: 0.9367 (mttt) cc_final: 0.8878 (tttm) REVERT: R 197 ASN cc_start: 0.8112 (t0) cc_final: 0.7822 (m-40) REVERT: R 198 MET cc_start: 0.9033 (mtm) cc_final: 0.8164 (mpp) REVERT: R 321 GLU cc_start: 0.8535 (tt0) cc_final: 0.8087 (tm-30) REVERT: S 74 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7749 (mm) REVERT: S 102 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8029 (ttm110) REVERT: S 126 PHE cc_start: 0.7918 (t80) cc_final: 0.7454 (t80) REVERT: S 251 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7708 (t80) REVERT: S 324 GLU cc_start: 0.7950 (pp20) cc_final: 0.7672 (tm-30) REVERT: T 126 PHE cc_start: 0.8017 (t80) cc_final: 0.7581 (t80) REVERT: T 198 MET cc_start: 0.8379 (mtp) cc_final: 0.8170 (mtm) REVERT: U 24 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8346 (tm-30) REVERT: U 112 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8322 (mmt-90) REVERT: V 145 SER cc_start: 0.9472 (m) cc_final: 0.9058 (t) REVERT: V 164 HIS cc_start: 0.8770 (t-90) cc_final: 0.8561 (t70) REVERT: V 316 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8665 (mp-120) REVERT: W 142 ASN cc_start: 0.8366 (t0) cc_final: 0.7889 (p0) outliers start: 147 outliers final: 101 residues processed: 489 average time/residue: 0.6167 time to fit residues: 510.5628 Evaluate side-chains 463 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 347 time to evaluate : 5.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 316 GLN Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 342 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 352 optimal weight: 8.9990 chunk 377 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 435 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS S 25 ASN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 316 GLN W 158 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 51876 Z= 0.338 Angle : 0.604 11.153 71055 Z= 0.314 Chirality : 0.040 0.208 7779 Planarity : 0.004 0.116 8346 Dihedral : 17.937 174.527 8982 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.16 % Favored : 93.43 % Rotamer: Outliers : 3.43 % Allowed : 22.09 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: 0.15 (0.12), residues: 5598 helix: 1.19 (0.11), residues: 2617 sheet: -0.91 (0.19), residues: 787 loop : -0.77 (0.14), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 73 HIS 0.017 0.001 HIS B 51 PHE 0.039 0.001 PHE R 138 TYR 0.029 0.002 TYR A 37 ARG 0.006 0.000 ARG W 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 342 time to evaluate : 6.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8512 (p0) cc_final: 0.8226 (p0) REVERT: A 209 GLN cc_start: 0.8986 (mt0) cc_final: 0.8615 (mt0) REVERT: B 118 ARG cc_start: 0.4504 (tmt170) cc_final: 0.3410 (mtp180) REVERT: B 187 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 244 TYR cc_start: 0.7559 (t80) cc_final: 0.7090 (t80) REVERT: E 77 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8688 (ttp-170) REVERT: F 77 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8993 (mtm110) REVERT: F 260 ASP cc_start: 0.9089 (t0) cc_final: 0.8823 (t0) REVERT: G 50 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8337 (mtpp) REVERT: G 77 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8108 (mtm-85) REVERT: I 26 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7967 (mmm) REVERT: I 358 TRP cc_start: 0.6026 (OUTLIER) cc_final: 0.5444 (p90) REVERT: J 112 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.4715 (p0) REVERT: L 95 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8754 (mp10) REVERT: P 40 TYR cc_start: 0.9367 (t80) cc_final: 0.8931 (t80) REVERT: P 125 MET cc_start: 0.8712 (mmm) cc_final: 0.8457 (mmm) REVERT: P 171 LYS cc_start: 0.9372 (mttt) cc_final: 0.8922 (tttt) REVERT: R 197 ASN cc_start: 0.8173 (t0) cc_final: 0.7897 (m-40) REVERT: R 198 MET cc_start: 0.9017 (mtm) cc_final: 0.8136 (mpp) REVERT: R 321 GLU cc_start: 0.8619 (tt0) cc_final: 0.8182 (tm-30) REVERT: S 25 ASN cc_start: 0.9035 (m-40) cc_final: 0.8683 (m-40) REVERT: S 74 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7750 (mm) REVERT: S 102 ARG cc_start: 0.8513 (ttm110) cc_final: 0.8034 (ttm110) REVERT: S 126 PHE cc_start: 0.8202 (t80) cc_final: 0.7670 (t80) REVERT: S 324 GLU cc_start: 0.7992 (pp20) cc_final: 0.7719 (tm-30) REVERT: T 126 PHE cc_start: 0.8262 (t80) cc_final: 0.7763 (t80) REVERT: T 210 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: U 24 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8432 (tm-30) REVERT: U 95 GLU cc_start: 0.8082 (pm20) cc_final: 0.7837 (pm20) REVERT: U 112 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8187 (mmt-90) REVERT: V 145 SER cc_start: 0.9483 (m) cc_final: 0.9060 (t) REVERT: V 164 HIS cc_start: 0.8790 (t-90) cc_final: 0.8567 (t70) REVERT: V 198 MET cc_start: 0.7798 (mtp) cc_final: 0.7302 (mtp) REVERT: V 234 CYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7820 (t) REVERT: W 41 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7795 (mmm) REVERT: W 142 ASN cc_start: 0.8423 (t0) cc_final: 0.7978 (p0) outliers start: 170 outliers final: 122 residues processed: 484 average time/residue: 0.6183 time to fit residues: 504.6656 Evaluate side-chains 473 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 338 time to evaluate : 5.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain Q residue 303 LYS Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 504 optimal weight: 7.9990 chunk 530 optimal weight: 0.9980 chunk 484 optimal weight: 4.9990 chunk 516 optimal weight: 0.9980 chunk 310 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 chunk 405 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 466 optimal weight: 0.5980 chunk 488 optimal weight: 4.9990 chunk 514 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 51876 Z= 0.245 Angle : 0.571 11.507 71055 Z= 0.296 Chirality : 0.039 0.214 7779 Planarity : 0.004 0.131 8346 Dihedral : 17.895 173.102 8979 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.73 % Favored : 93.87 % Rotamer: Outliers : 3.12 % Allowed : 22.46 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: 0.18 (0.12), residues: 5598 helix: 1.19 (0.11), residues: 2618 sheet: -0.89 (0.19), residues: 787 loop : -0.73 (0.14), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 73 HIS 0.019 0.001 HIS B 51 PHE 0.024 0.001 PHE F 234 TYR 0.038 0.001 TYR A 37 ARG 0.006 0.000 ARG W 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 352 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6629 (tpt) cc_final: 0.6379 (tpt) REVERT: A 39 MET cc_start: 0.9402 (tmm) cc_final: 0.9126 (tmm) REVERT: A 202 ASP cc_start: 0.8535 (p0) cc_final: 0.8264 (p0) REVERT: A 209 GLN cc_start: 0.9002 (mt0) cc_final: 0.8640 (mt0) REVERT: B 118 ARG cc_start: 0.4342 (tmt170) cc_final: 0.3408 (mmm-85) REVERT: B 187 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 33 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8577 (mm) REVERT: C 244 TYR cc_start: 0.7555 (t80) cc_final: 0.7156 (t80) REVERT: D 77 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8355 (ttp80) REVERT: E 77 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8732 (ttp-170) REVERT: F 77 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.9003 (mtm110) REVERT: F 260 ASP cc_start: 0.9068 (t0) cc_final: 0.8844 (t0) REVERT: F 268 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.8807 (p0) REVERT: G 50 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8335 (mtpp) REVERT: G 77 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8125 (mtm-85) REVERT: G 108 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8507 (tp) REVERT: G 221 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8216 (t80) REVERT: I 26 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8438 (mmm) REVERT: I 396 ASP cc_start: 0.7874 (t0) cc_final: 0.7429 (t70) REVERT: I 451 GLU cc_start: 0.9044 (tp30) cc_final: 0.8512 (tp30) REVERT: J 112 ASP cc_start: 0.5907 (OUTLIER) cc_final: 0.4603 (p0) REVERT: L 95 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8795 (mp10) REVERT: P 40 TYR cc_start: 0.9327 (t80) cc_final: 0.8867 (t80) REVERT: P 113 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8071 (p0) REVERT: P 171 LYS cc_start: 0.9372 (mttt) cc_final: 0.8921 (tttt) REVERT: Q 234 CYS cc_start: 0.8081 (t) cc_final: 0.7601 (p) REVERT: R 197 ASN cc_start: 0.8140 (t0) cc_final: 0.7850 (m-40) REVERT: R 198 MET cc_start: 0.9011 (mtm) cc_final: 0.8141 (mpp) REVERT: R 321 GLU cc_start: 0.8629 (tt0) cc_final: 0.8148 (tm-30) REVERT: S 25 ASN cc_start: 0.9029 (m-40) cc_final: 0.8656 (m-40) REVERT: S 74 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7738 (mm) REVERT: S 102 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8042 (ttm110) REVERT: S 126 PHE cc_start: 0.8155 (t80) cc_final: 0.7617 (t80) REVERT: S 251 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7714 (t80) REVERT: S 324 GLU cc_start: 0.7953 (pp20) cc_final: 0.7689 (tm-30) REVERT: T 126 PHE cc_start: 0.8283 (t80) cc_final: 0.7793 (t80) REVERT: T 210 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: U 24 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8434 (tm-30) REVERT: U 95 GLU cc_start: 0.8080 (pm20) cc_final: 0.7829 (pm20) REVERT: V 102 ARG cc_start: 0.8115 (tmm160) cc_final: 0.6630 (tmm160) REVERT: V 145 SER cc_start: 0.9495 (m) cc_final: 0.9070 (t) REVERT: V 164 HIS cc_start: 0.8774 (t-90) cc_final: 0.8560 (t70) REVERT: V 198 MET cc_start: 0.7806 (mtp) cc_final: 0.7283 (mtp) REVERT: W 41 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: W 142 ASN cc_start: 0.8475 (t0) cc_final: 0.8053 (p0) outliers start: 155 outliers final: 118 residues processed: 481 average time/residue: 0.6043 time to fit residues: 494.4498 Evaluate side-chains 474 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 339 time to evaluate : 5.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 410 MET Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain Q residue 303 LYS Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 339 optimal weight: 3.9990 chunk 546 optimal weight: 10.0000 chunk 333 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 379 optimal weight: 8.9990 chunk 572 optimal weight: 10.0000 chunk 527 optimal weight: 9.9990 chunk 456 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 352 optimal weight: 20.0000 chunk 279 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 ASN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 51876 Z= 0.271 Angle : 0.583 11.989 71055 Z= 0.302 Chirality : 0.040 0.206 7779 Planarity : 0.004 0.128 8346 Dihedral : 17.852 172.072 8974 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.11 % Favored : 93.50 % Rotamer: Outliers : 2.86 % Allowed : 22.82 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.17 (0.12), residues: 5598 helix: 1.18 (0.11), residues: 2618 sheet: -0.89 (0.19), residues: 787 loop : -0.72 (0.14), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP W 267 HIS 0.023 0.001 HIS B 51 PHE 0.038 0.001 PHE R 138 TYR 0.036 0.001 TYR A 37 ARG 0.009 0.000 ARG V 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11196 Ramachandran restraints generated. 5598 Oldfield, 0 Emsley, 5598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 341 time to evaluate : 5.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.9412 (tmm) cc_final: 0.9143 (tmm) REVERT: A 202 ASP cc_start: 0.8554 (p0) cc_final: 0.8291 (p0) REVERT: A 209 GLN cc_start: 0.9030 (mt0) cc_final: 0.8653 (mt0) REVERT: B 118 ARG cc_start: 0.4361 (tmt170) cc_final: 0.3415 (mmm-85) REVERT: B 119 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8134 (tt) REVERT: B 187 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7511 (tm-30) REVERT: C 33 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8631 (mm) REVERT: C 244 TYR cc_start: 0.7618 (t80) cc_final: 0.7233 (t80) REVERT: C 305 MET cc_start: 0.8520 (tpt) cc_final: 0.8305 (tpt) REVERT: D 15 TYR cc_start: 0.8500 (m-80) cc_final: 0.8244 (m-80) REVERT: D 77 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8348 (ttp80) REVERT: E 77 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8715 (ttp-170) REVERT: F 77 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.9003 (mtm110) REVERT: F 260 ASP cc_start: 0.9059 (t0) cc_final: 0.8838 (t0) REVERT: G 50 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8324 (mtpp) REVERT: G 77 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8120 (mtm-85) REVERT: G 108 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8503 (tp) REVERT: I 26 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8450 (mmm) REVERT: I 396 ASP cc_start: 0.7942 (t0) cc_final: 0.7501 (t70) REVERT: I 451 GLU cc_start: 0.9067 (tp30) cc_final: 0.8534 (tp30) REVERT: J 112 ASP cc_start: 0.5954 (OUTLIER) cc_final: 0.4663 (p0) REVERT: L 95 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8832 (mp10) REVERT: P 40 TYR cc_start: 0.9317 (t80) cc_final: 0.8908 (t80) REVERT: P 113 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8141 (p0) REVERT: P 171 LYS cc_start: 0.9368 (mttt) cc_final: 0.8919 (tttt) REVERT: Q 234 CYS cc_start: 0.8086 (t) cc_final: 0.7592 (p) REVERT: R 197 ASN cc_start: 0.8143 (t0) cc_final: 0.7879 (m-40) REVERT: R 198 MET cc_start: 0.9011 (mtm) cc_final: 0.8125 (mpp) REVERT: R 216 ASN cc_start: 0.8564 (m-40) cc_final: 0.7995 (m110) REVERT: R 321 GLU cc_start: 0.8635 (tt0) cc_final: 0.8139 (tm-30) REVERT: S 25 ASN cc_start: 0.9035 (m-40) cc_final: 0.8659 (m-40) REVERT: S 74 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7736 (mm) REVERT: S 102 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8034 (ttm110) REVERT: S 126 PHE cc_start: 0.8198 (t80) cc_final: 0.7643 (t80) REVERT: S 324 GLU cc_start: 0.7951 (pp20) cc_final: 0.7694 (tm-30) REVERT: T 210 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: U 24 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8470 (tm-30) REVERT: U 95 GLU cc_start: 0.8064 (pm20) cc_final: 0.7814 (pm20) REVERT: V 102 ARG cc_start: 0.8264 (tmm160) cc_final: 0.7816 (tmm160) REVERT: V 103 TYR cc_start: 0.7237 (t80) cc_final: 0.6786 (t80) REVERT: V 131 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7775 (mmm160) REVERT: V 145 SER cc_start: 0.9504 (m) cc_final: 0.9085 (t) REVERT: V 146 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8928 (mmmt) REVERT: V 164 HIS cc_start: 0.8789 (t-90) cc_final: 0.8572 (t70) REVERT: V 198 MET cc_start: 0.7896 (mtp) cc_final: 0.7398 (mtp) REVERT: W 41 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7927 (mmm) REVERT: W 109 TYR cc_start: 0.8833 (t80) cc_final: 0.8113 (t80) REVERT: W 142 ASN cc_start: 0.8490 (t0) cc_final: 0.8058 (p0) REVERT: W 164 HIS cc_start: 0.8373 (t70) cc_final: 0.7715 (p-80) outliers start: 142 outliers final: 119 residues processed: 461 average time/residue: 0.6057 time to fit residues: 473.3569 Evaluate side-chains 463 residues out of total 4961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 329 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 MET Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 410 MET Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 301 THR Chi-restraints excluded: chain Q residue 303 LYS Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 251 PHE Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 266 HIS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 275 LEU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 266 HIS Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 362 optimal weight: 6.9990 chunk 485 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 420 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 456 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 469 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** T 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN W 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.082079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059524 restraints weight = 174234.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.061334 restraints weight = 73816.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.062517 restraints weight = 43348.783| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 51876 Z= 0.308 Angle : 0.657 59.199 71055 Z= 0.362 Chirality : 0.042 1.234 7779 Planarity : 0.004 0.106 8346 Dihedral : 17.853 172.069 8974 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.09 % Favored : 93.52 % Rotamer: Outliers : 3.08 % Allowed : 22.62 % Favored : 74.30 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.17 (0.12), residues: 5598 helix: 1.18 (0.10), residues: 2618 sheet: -0.88 (0.19), residues: 787 loop : -0.72 (0.14), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP W 267 HIS 0.021 0.001 HIS B 51 PHE 0.025 0.001 PHE R 138 TYR 0.035 0.001 TYR I 329 ARG 0.079 0.000 ARG I 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10823.54 seconds wall clock time: 199 minutes 6.82 seconds (11946.82 seconds total)