Starting phenix.real_space_refine on Fri Mar 15 20:20:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/03_2024/5aey_2850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/03_2024/5aey_2850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/03_2024/5aey_2850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/03_2024/5aey_2850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/03_2024/5aey_2850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/03_2024/5aey_2850_updated.pdb" } resolution = 4.3 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 40 5.16 5 C 7950 2.51 5 N 2140 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12675 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "B" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "C" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "D" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "E" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.48, per 1000 atoms: 0.59 Number of scatterers: 12675 At special positions: 0 Unit cell: (78.11, 98.44, 181.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 15 15.00 O 2530 8.00 N 2140 7.00 C 7950 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: 5.23 Conformation dependent library (CDL) restraints added in 2.5 seconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 15 sheets defined 38.1% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.942A pdb=" N GLN A 73 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.816A pdb=" N PHE A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 5.179A pdb=" N GLU A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 4.009A pdb=" N SER A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 245 through 269 removed outlier: 3.693A pdb=" N GLU A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 4.082A pdb=" N CYS A 287 " --> pdb=" O GLU A 284 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP A 288 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 292 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 317 removed outlier: 5.069A pdb=" N LEU A 311 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.957A pdb=" N GLN B 73 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 116 through 127 removed outlier: 3.816A pdb=" N PHE B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 158 removed outlier: 5.183A pdb=" N GLU B 155 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 4.030A pdb=" N SER B 204 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 245 through 269 removed outlier: 3.661A pdb=" N GLU B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 4.104A pdb=" N CYS B 287 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP B 288 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 292 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 317 removed outlier: 5.064A pdb=" N LEU B 311 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.957A pdb=" N GLN C 73 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 88 Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.818A pdb=" N PHE C 126 " --> pdb=" O LYS C 122 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 158 removed outlier: 5.179A pdb=" N GLU C 155 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 removed outlier: 4.031A pdb=" N SER C 204 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS C 207 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 227 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 245 through 269 removed outlier: 3.650A pdb=" N GLU C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 removed outlier: 4.120A pdb=" N CYS C 287 " --> pdb=" O GLU C 284 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP C 288 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 292 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 317 removed outlier: 5.060A pdb=" N LEU C 311 " --> pdb=" O GLN C 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.960A pdb=" N GLN D 73 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.818A pdb=" N PHE D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 158 removed outlier: 5.176A pdb=" N GLU D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 212 removed outlier: 4.037A pdb=" N SER D 204 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS D 207 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 227 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 245 through 269 removed outlier: 3.660A pdb=" N GLU D 250 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU D 269 " --> pdb=" O ASN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 4.131A pdb=" N CYS D 287 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D 292 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 317 removed outlier: 5.056A pdb=" N LEU D 311 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.949A pdb=" N GLN E 73 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 88 Processing helix chain 'E' and resid 116 through 127 removed outlier: 3.817A pdb=" N PHE E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 158 removed outlier: 5.184A pdb=" N GLU E 155 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 212 removed outlier: 4.039A pdb=" N SER E 204 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS E 207 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 227 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 245 through 269 removed outlier: 3.648A pdb=" N GLU E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 261 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 269 " --> pdb=" O ASN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 294 removed outlier: 4.129A pdb=" N CYS E 287 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASP E 288 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS E 292 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 317 removed outlier: 5.059A pdb=" N LEU E 311 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 22 through 29 removed outlier: 5.514A pdb=" N GLN A 17 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU A 2 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 97 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 5 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL A 99 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP A 7 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR A 101 " --> pdb=" O ASP A 7 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 49 Processing sheet with id= C, first strand: chain 'A' and resid 275 through 279 removed outlier: 6.306A pdb=" N MET A 182 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE A 188 " --> pdb=" O MET A 182 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 22 through 29 removed outlier: 5.454A pdb=" N GLN B 17 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 2 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASP B 97 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE B 5 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL B 99 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP B 7 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR B 101 " --> pdb=" O ASP B 7 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 47 through 49 Processing sheet with id= F, first strand: chain 'B' and resid 275 through 279 removed outlier: 6.304A pdb=" N MET B 182 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE B 188 " --> pdb=" O MET B 182 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 22 through 29 removed outlier: 5.483A pdb=" N GLN C 17 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU C 2 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP C 97 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 5 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL C 99 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASP C 7 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR C 101 " --> pdb=" O ASP C 7 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 49 Processing sheet with id= I, first strand: chain 'C' and resid 275 through 279 removed outlier: 6.307A pdb=" N MET C 182 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE C 188 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 22 through 29 removed outlier: 5.496A pdb=" N GLN D 17 " --> pdb=" O LEU D 2 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU D 2 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP D 97 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE D 5 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL D 99 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP D 7 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR D 101 " --> pdb=" O ASP D 7 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 47 through 49 Processing sheet with id= L, first strand: chain 'D' and resid 275 through 279 removed outlier: 6.305A pdb=" N MET D 182 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE D 188 " --> pdb=" O MET D 182 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 22 through 29 removed outlier: 5.481A pdb=" N GLN E 17 " --> pdb=" O LEU E 2 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU E 2 " --> pdb=" O GLN E 17 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP E 97 " --> pdb=" O VAL E 3 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE E 5 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL E 99 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP E 7 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR E 101 " --> pdb=" O ASP E 7 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 47 through 49 Processing sheet with id= O, first strand: chain 'E' and resid 275 through 279 removed outlier: 6.306A pdb=" N MET E 182 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE E 188 " --> pdb=" O MET E 182 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2456 1.32 - 1.45: 3160 1.45 - 1.57: 7164 1.57 - 1.70: 40 1.70 - 1.82: 70 Bond restraints: 12890 Sorted by residual: bond pdb=" C PHE B 4 " pdb=" N ILE B 5 " ideal model delta sigma weight residual 1.329 1.444 -0.115 1.37e-02 5.33e+03 7.07e+01 bond pdb=" N3B ANP B 500 " pdb=" PG ANP B 500 " ideal model delta sigma weight residual 1.795 1.643 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N3B ANP C 500 " pdb=" PG ANP C 500 " ideal model delta sigma weight residual 1.795 1.645 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" N3B ANP D 500 " pdb=" PG ANP D 500 " ideal model delta sigma weight residual 1.795 1.647 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" N3B ANP E 500 " pdb=" PG ANP E 500 " ideal model delta sigma weight residual 1.795 1.648 0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 12885 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.67: 379 106.67 - 113.42: 6542 113.42 - 120.18: 5130 120.18 - 126.93: 5291 126.93 - 133.68: 153 Bond angle restraints: 17495 Sorted by residual: angle pdb=" C PHE B 4 " pdb=" N ILE B 5 " pdb=" CA ILE B 5 " ideal model delta sigma weight residual 123.11 112.68 10.43 1.36e+00 5.41e-01 5.88e+01 angle pdb=" N VAL E 66 " pdb=" CA VAL E 66 " pdb=" CB VAL E 66 " ideal model delta sigma weight residual 110.53 117.03 -6.50 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N VAL A 66 " pdb=" CA VAL A 66 " pdb=" CB VAL A 66 " ideal model delta sigma weight residual 110.53 117.02 -6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" N VAL C 66 " pdb=" CA VAL C 66 " pdb=" CB VAL C 66 " ideal model delta sigma weight residual 110.53 116.91 -6.38 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N VAL D 66 " pdb=" CA VAL D 66 " pdb=" CB VAL D 66 " ideal model delta sigma weight residual 110.53 116.89 -6.36 1.09e+00 8.42e-01 3.40e+01 ... (remaining 17490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 7054 30.21 - 60.41: 731 60.41 - 90.62: 65 90.62 - 120.83: 0 120.83 - 151.03: 5 Dihedral angle restraints: 7855 sinusoidal: 3230 harmonic: 4625 Sorted by residual: dihedral pdb=" CA LEU B 317 " pdb=" C LEU B 317 " pdb=" N ILE B 318 " pdb=" CA ILE B 318 " ideal model delta harmonic sigma weight residual 180.00 142.63 37.37 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA LEU A 317 " pdb=" C LEU A 317 " pdb=" N ILE A 318 " pdb=" CA ILE A 318 " ideal model delta harmonic sigma weight residual 180.00 142.75 37.25 0 5.00e+00 4.00e-02 5.55e+01 dihedral pdb=" CA LEU D 317 " pdb=" C LEU D 317 " pdb=" N ILE D 318 " pdb=" CA ILE D 318 " ideal model delta harmonic sigma weight residual 180.00 142.89 37.11 0 5.00e+00 4.00e-02 5.51e+01 ... (remaining 7852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1180 0.073 - 0.146: 514 0.146 - 0.219: 185 0.219 - 0.292: 84 0.292 - 0.365: 57 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA ARG A 262 " pdb=" N ARG A 262 " pdb=" C ARG A 262 " pdb=" CB ARG A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ASN D 268 " pdb=" N ASN D 268 " pdb=" C ASN D 268 " pdb=" CB ASN D 268 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA PHE B 46 " pdb=" N PHE B 46 " pdb=" C PHE B 46 " pdb=" CB PHE B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 2017 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 107 " -0.046 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR E 107 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR E 107 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 107 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR E 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 107 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 107 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 107 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 107 " -0.046 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR A 107 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 107 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 107 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 107 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 107 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 107 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 107 " 0.042 2.00e-02 2.50e+03 2.23e-02 9.95e+00 pdb=" CG TYR D 107 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR D 107 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 107 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 107 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 107 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 107 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 107 " 0.018 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 844 2.74 - 3.28: 13308 3.28 - 3.82: 21668 3.82 - 4.36: 26506 4.36 - 4.90: 41457 Nonbonded interactions: 103783 Sorted by model distance: nonbonded pdb=" N ARG A 297 " pdb=" OD2 ASP C 241 " model vdw 2.197 2.520 nonbonded pdb=" N ARG C 297 " pdb=" OD2 ASP E 241 " model vdw 2.220 2.520 nonbonded pdb=" N ARG B 297 " pdb=" OD2 ASP D 241 " model vdw 2.222 2.520 nonbonded pdb=" O ASP B 164 " pdb=" N GLY B 183 " model vdw 2.303 2.520 nonbonded pdb=" O ASP E 164 " pdb=" N GLY E 183 " model vdw 2.303 2.520 ... (remaining 103778 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.430 Check model and map are aligned: 0.200 Set scattering table: 0.150 Process input model: 38.390 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.011 0.152 12890 Z= 0.737 Angle : 1.714 14.993 17495 Z= 1.035 Chirality : 0.110 0.365 2020 Planarity : 0.006 0.047 2220 Dihedral : 22.055 151.032 4875 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 2.85 % Allowed : 8.67 % Favored : 88.48 % Rotamer: Outliers : 18.45 % Allowed : 22.90 % Favored : 58.66 % Cbeta Deviations : 2.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.68 % 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: -3.27 (0.18), residues: 1580 helix: -2.13 (0.17), residues: 555 sheet: -1.14 (0.26), residues: 365 loop : -2.70 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 72 HIS 0.007 0.002 HIS E 293 PHE 0.028 0.004 PHE A 138 TYR 0.047 0.007 TYR E 107 ARG 0.004 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 370 time to evaluate : 1.622 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: A 1 MET cc_start: 0.8575 (mpp) cc_final: 0.7635 (ttt) REVERT: A 101 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7580 (t) REVERT: A 106 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8362 (tp30) REVERT: A 107 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: A 111 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8560 (p0) REVERT: A 121 ARG cc_start: 0.8905 (mtp85) cc_final: 0.8635 (mtp85) REVERT: A 148 GLU cc_start: 0.5993 (tt0) cc_final: 0.5241 (tt0) REVERT: A 158 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8447 (mm-40) REVERT: A 194 ASP cc_start: 0.7425 (t0) cc_final: 0.7049 (t0) REVERT: A 238 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8634 (mmt180) REVERT: A 261 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8263 (tp40) REVERT: A 262 ARG cc_start: 0.8642 (ptt180) cc_final: 0.8301 (ptm160) REVERT: A 292 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (ptpt) REVERT: A 302 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: A 308 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8161 (tp-100) REVERT: A 315 MET cc_start: 0.8961 (mtp) cc_final: 0.8732 (mtm) REVERT: B 1 MET cc_start: 0.8708 (mpp) cc_final: 0.8105 (ttt) REVERT: B 54 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7502 (pp30) REVERT: B 101 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.6890 (t) REVERT: B 106 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8125 (tp30) REVERT: B 107 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: B 111 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8429 (p0) REVERT: B 125 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7358 (t0) REVERT: B 148 GLU cc_start: 0.5037 (tt0) cc_final: 0.4498 (tt0) REVERT: B 194 ASP cc_start: 0.7018 (t0) cc_final: 0.6723 (t0) REVERT: B 208 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7958 (t70) REVERT: B 234 TYR cc_start: 0.9070 (t80) cc_final: 0.8284 (t80) REVERT: B 261 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8264 (tp-100) REVERT: B 292 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8209 (ptpt) REVERT: B 302 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: B 316 TYR cc_start: 0.8488 (t80) cc_final: 0.8189 (t80) REVERT: C 1 MET cc_start: 0.8735 (mpp) cc_final: 0.8212 (ttt) REVERT: C 31 SER cc_start: 0.7913 (OUTLIER) cc_final: 0.7660 (t) REVERT: C 74 TYR cc_start: 0.8150 (m-80) cc_final: 0.7668 (m-80) REVERT: C 97 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: C 101 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7049 (t) REVERT: C 106 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8002 (tp30) REVERT: C 107 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: C 111 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8218 (p0) REVERT: C 139 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.6874 (p) REVERT: C 140 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8222 (pt) REVERT: C 148 GLU cc_start: 0.5864 (tt0) cc_final: 0.5350 (tt0) REVERT: C 194 ASP cc_start: 0.7218 (t0) cc_final: 0.6911 (t70) REVERT: C 219 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8644 (p) REVERT: C 234 TYR cc_start: 0.8973 (t80) cc_final: 0.8667 (t80) REVERT: C 247 ILE cc_start: 0.8692 (tt) cc_final: 0.8435 (tt) REVERT: C 262 ARG cc_start: 0.8758 (ptt180) cc_final: 0.8490 (mtm-85) REVERT: C 292 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8151 (pttt) REVERT: D 1 MET cc_start: 0.8758 (mpp) cc_final: 0.8316 (ttt) REVERT: D 31 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7427 (t) REVERT: D 53 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: D 74 TYR cc_start: 0.7967 (m-80) cc_final: 0.7452 (m-80) REVERT: D 101 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7122 (t) REVERT: D 106 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8223 (tp30) REVERT: D 121 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8300 (mtp85) REVERT: D 125 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7555 (t0) REVERT: D 148 GLU cc_start: 0.5630 (tt0) cc_final: 0.4961 (tt0) REVERT: D 158 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8694 (mm-40) REVERT: D 216 LYS cc_start: 0.9041 (ttmp) cc_final: 0.8786 (tttp) REVERT: D 261 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8600 (tp40) REVERT: D 292 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8277 (mmtm) REVERT: D 310 ASP cc_start: 0.8549 (m-30) cc_final: 0.8253 (m-30) REVERT: E 1 MET cc_start: 0.8977 (mpp) cc_final: 0.8545 (ttt) REVERT: E 31 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.7155 (t) REVERT: E 40 PHE cc_start: 0.7398 (t80) cc_final: 0.7087 (t80) REVERT: E 54 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6499 (pp30) REVERT: E 106 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8276 (tp30) REVERT: E 110 ARG cc_start: 0.7393 (mmp80) cc_final: 0.7101 (ttt180) REVERT: E 121 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8053 (mtp85) REVERT: E 158 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8638 (mm-40) REVERT: E 247 ILE cc_start: 0.8774 (tt) cc_final: 0.8531 (tp) REVERT: E 261 GLN cc_start: 0.9309 (tp-100) cc_final: 0.8711 (tp40) REVERT: E 262 ARG cc_start: 0.8780 (ptt180) cc_final: 0.8469 (mtt180) REVERT: E 296 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6700 (mp) REVERT: E 302 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7738 (m-80) outliers start: 261 outliers final: 78 residues processed: 576 average time/residue: 0.2890 time to fit residues: 224.1647 Evaluate side-chains 345 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 231 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 50.0000 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 83 HIS A 118 ASN A 261 GLN B 83 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 83 HIS ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 83 HIS D 115 ASN D 118 ASN D 261 GLN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 83 HIS E 115 ASN E 118 ASN E 125 ASN E 261 GLN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12890 Z= 0.268 Angle : 0.797 8.690 17495 Z= 0.413 Chirality : 0.047 0.215 2020 Planarity : 0.005 0.076 2220 Dihedral : 13.627 170.300 1860 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.94 % Favored : 89.43 % Rotamer: Outliers : 0.21 % Allowed : 5.09 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.05 (0.19), residues: 1580 helix: -0.98 (0.20), residues: 565 sheet: -0.12 (0.28), residues: 335 loop : -2.31 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 72 HIS 0.009 0.002 HIS C 275 PHE 0.018 0.002 PHE A 4 TYR 0.031 0.002 TYR B 107 ARG 0.007 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 358 time to evaluate : 1.709 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 74 TYR cc_start: 0.8302 (m-80) cc_final: 0.7924 (m-10) REVERT: A 148 GLU cc_start: 0.5958 (tt0) cc_final: 0.5462 (tt0) REVERT: A 176 LEU cc_start: 0.8636 (tt) cc_final: 0.7835 (tt) REVERT: A 194 ASP cc_start: 0.7101 (t0) cc_final: 0.6460 (p0) REVERT: A 197 LEU cc_start: 0.8263 (mp) cc_final: 0.7944 (mp) REVERT: A 292 LYS cc_start: 0.8116 (pptt) cc_final: 0.7847 (ptpt) REVERT: B 1 MET cc_start: 0.9022 (mpp) cc_final: 0.8381 (ttt) REVERT: B 16 TRP cc_start: 0.8748 (p-90) cc_final: 0.8230 (p90) REVERT: B 24 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8890 (mtpp) REVERT: B 74 TYR cc_start: 0.7807 (m-80) cc_final: 0.7376 (m-10) REVERT: B 126 PHE cc_start: 0.7623 (m-10) cc_final: 0.7329 (m-80) REVERT: B 142 ASP cc_start: 0.9139 (t70) cc_final: 0.8638 (m-30) REVERT: B 148 GLU cc_start: 0.4898 (tt0) cc_final: 0.4627 (tt0) REVERT: B 176 LEU cc_start: 0.8685 (tt) cc_final: 0.7831 (tt) REVERT: B 194 ASP cc_start: 0.6863 (t0) cc_final: 0.6363 (p0) REVERT: B 197 LEU cc_start: 0.7442 (mp) cc_final: 0.7099 (mp) REVERT: B 234 TYR cc_start: 0.8980 (t80) cc_final: 0.7941 (t80) REVERT: B 261 GLN cc_start: 0.8626 (tp40) cc_final: 0.8329 (tp-100) REVERT: B 265 ASN cc_start: 0.8270 (m110) cc_final: 0.8058 (m-40) REVERT: B 292 LYS cc_start: 0.8105 (pptt) cc_final: 0.7825 (ptpt) REVERT: C 1 MET cc_start: 0.8861 (mpp) cc_final: 0.8384 (ttt) REVERT: C 24 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8881 (mttp) REVERT: C 58 ASP cc_start: 0.8260 (t0) cc_final: 0.7957 (t0) REVERT: C 74 TYR cc_start: 0.8032 (m-80) cc_final: 0.7477 (m-80) REVERT: C 111 ASN cc_start: 0.8650 (m-40) cc_final: 0.8432 (p0) REVERT: C 142 ASP cc_start: 0.8956 (t70) cc_final: 0.8751 (t0) REVERT: C 148 GLU cc_start: 0.4793 (tt0) cc_final: 0.4408 (tt0) REVERT: C 194 ASP cc_start: 0.7221 (t0) cc_final: 0.6695 (p0) REVERT: C 234 TYR cc_start: 0.8576 (t80) cc_final: 0.8285 (t80) REVERT: C 292 LYS cc_start: 0.8033 (pptt) cc_final: 0.7719 (ptpt) REVERT: D 1 MET cc_start: 0.8878 (mpp) cc_final: 0.8403 (ttt) REVERT: D 16 TRP cc_start: 0.8806 (p-90) cc_final: 0.8421 (p90) REVERT: D 24 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8972 (mtpp) REVERT: D 58 ASP cc_start: 0.8246 (t0) cc_final: 0.7922 (t0) REVERT: D 74 TYR cc_start: 0.8011 (m-80) cc_final: 0.7699 (m-80) REVERT: D 104 LEU cc_start: 0.8754 (mt) cc_final: 0.8514 (mp) REVERT: D 142 ASP cc_start: 0.9033 (t70) cc_final: 0.8720 (t0) REVERT: D 148 GLU cc_start: 0.5063 (tt0) cc_final: 0.4658 (tt0) REVERT: D 176 LEU cc_start: 0.8494 (tt) cc_final: 0.7845 (tt) REVERT: D 194 ASP cc_start: 0.6361 (t70) cc_final: 0.5874 (p0) REVERT: D 197 LEU cc_start: 0.7887 (mp) cc_final: 0.7537 (mp) REVERT: D 292 LYS cc_start: 0.8448 (pptt) cc_final: 0.8186 (ptpt) REVERT: E 1 MET cc_start: 0.8941 (mpp) cc_final: 0.8484 (ttt) REVERT: E 58 ASP cc_start: 0.8315 (t0) cc_final: 0.8039 (t0) REVERT: E 106 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8102 (mm-30) REVERT: E 110 ARG cc_start: 0.7556 (mmp80) cc_final: 0.7239 (ttt180) REVERT: E 117 GLU cc_start: 0.8790 (tp30) cc_final: 0.8491 (tp30) REVERT: E 121 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7722 (mtp85) REVERT: E 148 GLU cc_start: 0.5419 (tt0) cc_final: 0.5155 (tt0) REVERT: E 176 LEU cc_start: 0.8380 (tt) cc_final: 0.7547 (tt) REVERT: E 194 ASP cc_start: 0.7237 (t0) cc_final: 0.6526 (p0) REVERT: E 315 MET cc_start: 0.8437 (mtm) cc_final: 0.7750 (ptp) outliers start: 3 outliers final: 2 residues processed: 361 average time/residue: 0.3018 time to fit residues: 146.8105 Evaluate side-chains 242 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 152 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 115 ASN B 118 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 115 ASN D 253 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12890 Z= 0.275 Angle : 0.730 8.463 17495 Z= 0.384 Chirality : 0.046 0.250 2020 Planarity : 0.005 0.045 2220 Dihedral : 13.576 179.581 1860 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.63 % Favored : 89.05 % Rotamer: Outliers : 0.28 % Allowed : 3.60 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.85 (0.20), residues: 1580 helix: -0.98 (0.20), residues: 595 sheet: -0.17 (0.26), residues: 385 loop : -2.07 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 72 HIS 0.006 0.002 HIS A 228 PHE 0.012 0.002 PHE B 138 TYR 0.016 0.002 TYR E 107 ARG 0.005 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 294 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7992 (m-80) cc_final: 0.7480 (m-80) REVERT: A 106 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8122 (mm-30) REVERT: A 148 GLU cc_start: 0.5184 (tt0) cc_final: 0.4654 (tt0) REVERT: A 292 LYS cc_start: 0.8244 (pptt) cc_final: 0.7911 (ptpt) REVERT: A 315 MET cc_start: 0.8561 (mtm) cc_final: 0.8108 (ptp) REVERT: B 1 MET cc_start: 0.9040 (mpp) cc_final: 0.8405 (ttt) REVERT: B 48 TYR cc_start: 0.9095 (m-80) cc_final: 0.8427 (m-80) REVERT: B 74 TYR cc_start: 0.7438 (m-80) cc_final: 0.7172 (m-10) REVERT: B 106 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8195 (mm-30) REVERT: B 142 ASP cc_start: 0.9076 (t70) cc_final: 0.8769 (m-30) REVERT: B 148 GLU cc_start: 0.4505 (tt0) cc_final: 0.4101 (tt0) REVERT: B 234 TYR cc_start: 0.8978 (t80) cc_final: 0.8040 (t80) REVERT: B 292 LYS cc_start: 0.8085 (pptt) cc_final: 0.7770 (mtmt) REVERT: C 1 MET cc_start: 0.8720 (mpp) cc_final: 0.8224 (ttt) REVERT: C 24 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8974 (mttt) REVERT: C 58 ASP cc_start: 0.8295 (t70) cc_final: 0.7967 (t0) REVERT: C 74 TYR cc_start: 0.7832 (m-80) cc_final: 0.7229 (m-80) REVERT: C 106 GLU cc_start: 0.8418 (tp30) cc_final: 0.8205 (tp30) REVERT: C 148 GLU cc_start: 0.4629 (tt0) cc_final: 0.4104 (tt0) REVERT: C 194 ASP cc_start: 0.7117 (t0) cc_final: 0.6719 (p0) REVERT: C 234 TYR cc_start: 0.8603 (t80) cc_final: 0.8330 (t80) REVERT: D 1 MET cc_start: 0.8915 (mpp) cc_final: 0.8352 (ttt) REVERT: D 24 LYS cc_start: 0.9261 (mmmt) cc_final: 0.9046 (mttt) REVERT: D 58 ASP cc_start: 0.8274 (t70) cc_final: 0.7961 (t0) REVERT: D 74 TYR cc_start: 0.7978 (m-80) cc_final: 0.7733 (m-80) REVERT: D 148 GLU cc_start: 0.4708 (tt0) cc_final: 0.4289 (tt0) REVERT: D 194 ASP cc_start: 0.6364 (t70) cc_final: 0.6158 (p0) REVERT: D 197 LEU cc_start: 0.7864 (mp) cc_final: 0.7612 (mp) REVERT: D 214 ARG cc_start: 0.8079 (mtm180) cc_final: 0.7714 (ttm170) REVERT: D 292 LYS cc_start: 0.8443 (pptt) cc_final: 0.8141 (mtmt) REVERT: D 315 MET cc_start: 0.8641 (mtm) cc_final: 0.8404 (mtt) REVERT: E 1 MET cc_start: 0.8925 (mpp) cc_final: 0.8542 (ttt) REVERT: E 58 ASP cc_start: 0.8197 (t70) cc_final: 0.7911 (t0) REVERT: E 104 LEU cc_start: 0.8590 (mt) cc_final: 0.8377 (mp) REVERT: E 106 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8070 (mm-30) REVERT: E 110 ARG cc_start: 0.7307 (mmp80) cc_final: 0.6933 (ttt180) REVERT: E 194 ASP cc_start: 0.7214 (t0) cc_final: 0.6500 (p0) REVERT: E 197 LEU cc_start: 0.7875 (mt) cc_final: 0.7522 (mt) REVERT: E 315 MET cc_start: 0.8557 (mtm) cc_final: 0.8165 (mtt) outliers start: 4 outliers final: 0 residues processed: 298 average time/residue: 0.2579 time to fit residues: 107.6506 Evaluate side-chains 206 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 67 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 141 optimal weight: 40.0000 chunk 149 optimal weight: 30.0000 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 overall best weight: 10.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 GLN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 118 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 78 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 118 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12890 Z= 0.316 Angle : 0.747 7.693 17495 Z= 0.395 Chirality : 0.046 0.189 2020 Planarity : 0.005 0.066 2220 Dihedral : 13.626 179.058 1860 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.57 % Favored : 89.11 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.71 (0.20), residues: 1580 helix: -0.68 (0.22), residues: 520 sheet: 0.15 (0.28), residues: 325 loop : -2.07 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 16 HIS 0.006 0.002 HIS E 293 PHE 0.013 0.002 PHE E 138 TYR 0.036 0.002 TYR B 107 ARG 0.005 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8154 (t0) cc_final: 0.7819 (t0) REVERT: A 74 TYR cc_start: 0.8060 (m-80) cc_final: 0.7848 (m-80) REVERT: A 208 ASP cc_start: 0.8284 (m-30) cc_final: 0.7755 (t70) REVERT: A 292 LYS cc_start: 0.8306 (pptt) cc_final: 0.8002 (ptpt) REVERT: B 1 MET cc_start: 0.8958 (mpp) cc_final: 0.8403 (ttt) REVERT: B 48 TYR cc_start: 0.8997 (m-80) cc_final: 0.8255 (m-80) REVERT: B 142 ASP cc_start: 0.9088 (t70) cc_final: 0.8824 (m-30) REVERT: B 234 TYR cc_start: 0.8938 (t80) cc_final: 0.8119 (t80) REVERT: B 292 LYS cc_start: 0.8225 (pptt) cc_final: 0.7949 (mtmt) REVERT: C 1 MET cc_start: 0.8641 (mpp) cc_final: 0.8206 (ttt) REVERT: C 74 TYR cc_start: 0.7567 (m-80) cc_final: 0.7232 (m-80) REVERT: C 117 GLU cc_start: 0.8825 (tp30) cc_final: 0.8609 (tp30) REVERT: C 148 GLU cc_start: 0.4699 (tt0) cc_final: 0.4370 (pt0) REVERT: C 194 ASP cc_start: 0.7084 (t0) cc_final: 0.6718 (p0) REVERT: C 234 TYR cc_start: 0.8589 (t80) cc_final: 0.8328 (t80) REVERT: D 1 MET cc_start: 0.8867 (mpp) cc_final: 0.8330 (ttt) REVERT: D 58 ASP cc_start: 0.8165 (t70) cc_final: 0.7869 (t0) REVERT: D 197 LEU cc_start: 0.7708 (mp) cc_final: 0.7464 (mp) REVERT: D 292 LYS cc_start: 0.8478 (pptt) cc_final: 0.8185 (mttp) REVERT: E 1 MET cc_start: 0.8937 (mpp) cc_final: 0.8588 (ttt) REVERT: E 58 ASP cc_start: 0.8218 (t70) cc_final: 0.7966 (t0) REVERT: E 110 ARG cc_start: 0.7361 (mmp80) cc_final: 0.6976 (ttt180) REVERT: E 194 ASP cc_start: 0.6377 (t70) cc_final: 0.5832 (p0) REVERT: E 197 LEU cc_start: 0.7936 (mt) cc_final: 0.7677 (mt) REVERT: E 315 MET cc_start: 0.8605 (mtm) cc_final: 0.8309 (mtt) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2607 time to fit residues: 94.5165 Evaluate side-chains 197 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.0570 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 37 optimal weight: 30.0000 chunk 50 optimal weight: 4.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 265 ASN B 115 ASN B 118 ASN B 253 ASN B 308 GLN C 78 ASN C 308 GLN D 17 GLN D 78 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN E 115 ASN E 118 ASN E 308 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12890 Z= 0.182 Angle : 0.666 7.143 17495 Z= 0.348 Chirality : 0.043 0.249 2020 Planarity : 0.004 0.043 2220 Dihedral : 13.195 177.717 1860 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.38 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.75 (0.20), residues: 1580 helix: -0.97 (0.21), residues: 585 sheet: 0.14 (0.27), residues: 355 loop : -2.03 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 72 HIS 0.005 0.001 HIS B 275 PHE 0.012 0.002 PHE C 138 TYR 0.024 0.002 TYR C 107 ARG 0.006 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8083 (t0) cc_final: 0.7587 (t0) REVERT: A 208 ASP cc_start: 0.8209 (m-30) cc_final: 0.7705 (t70) REVERT: A 292 LYS cc_start: 0.8355 (pptt) cc_final: 0.8043 (mtmt) REVERT: B 1 MET cc_start: 0.8945 (mpp) cc_final: 0.8423 (ttt) REVERT: B 48 TYR cc_start: 0.8949 (m-80) cc_final: 0.8344 (m-80) REVERT: B 54 GLN cc_start: 0.8439 (pt0) cc_final: 0.7992 (pt0) REVERT: B 106 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8166 (mm-30) REVERT: B 120 GLU cc_start: 0.8681 (pm20) cc_final: 0.8278 (tp30) REVERT: B 142 ASP cc_start: 0.9094 (t70) cc_final: 0.8745 (m-30) REVERT: B 148 GLU cc_start: 0.5221 (tt0) cc_final: 0.4788 (tt0) REVERT: B 168 ILE cc_start: 0.8517 (mp) cc_final: 0.8274 (mm) REVERT: B 234 TYR cc_start: 0.8870 (t80) cc_final: 0.8074 (t80) REVERT: B 292 LYS cc_start: 0.8249 (pptt) cc_final: 0.7909 (mttp) REVERT: C 1 MET cc_start: 0.8667 (mpp) cc_final: 0.8209 (ttt) REVERT: C 58 ASP cc_start: 0.8302 (t70) cc_final: 0.8037 (t0) REVERT: D 1 MET cc_start: 0.8897 (mpp) cc_final: 0.8497 (ttt) REVERT: D 58 ASP cc_start: 0.8238 (t70) cc_final: 0.7949 (t0) REVERT: D 74 TYR cc_start: 0.7407 (m-80) cc_final: 0.6963 (m-80) REVERT: D 148 GLU cc_start: 0.5241 (tt0) cc_final: 0.4889 (tt0) REVERT: D 158 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8233 (mm110) REVERT: D 214 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7934 (ttm110) REVERT: D 234 TYR cc_start: 0.8489 (t80) cc_final: 0.8118 (t80) REVERT: D 292 LYS cc_start: 0.8437 (pptt) cc_final: 0.8098 (mttp) REVERT: E 1 MET cc_start: 0.8850 (mpp) cc_final: 0.8597 (ttt) REVERT: E 58 ASP cc_start: 0.8087 (t70) cc_final: 0.7833 (t0) REVERT: E 110 ARG cc_start: 0.7115 (mmp80) cc_final: 0.6709 (ttt180) REVERT: E 176 LEU cc_start: 0.8633 (tt) cc_final: 0.8164 (tt) REVERT: E 194 ASP cc_start: 0.6340 (t70) cc_final: 0.5883 (p0) REVERT: E 197 LEU cc_start: 0.8046 (mt) cc_final: 0.7780 (mt) REVERT: E 292 LYS cc_start: 0.8720 (ptpt) cc_final: 0.8439 (mmtm) REVERT: E 315 MET cc_start: 0.8486 (mtm) cc_final: 0.8233 (mtt) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2541 time to fit residues: 103.6095 Evaluate side-chains 213 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 149 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 253 ASN A 265 ASN B 15 GLN B 17 GLN C 78 ASN D 78 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12890 Z= 0.212 Angle : 0.672 7.306 17495 Z= 0.352 Chirality : 0.044 0.221 2020 Planarity : 0.005 0.078 2220 Dihedral : 13.012 177.855 1860 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.94 % Favored : 89.75 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.20), residues: 1580 helix: -1.07 (0.20), residues: 595 sheet: 0.11 (0.27), residues: 360 loop : -1.99 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 72 HIS 0.005 0.001 HIS D 26 PHE 0.011 0.002 PHE E 138 TYR 0.022 0.002 TYR D 107 ARG 0.004 0.001 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8088 (t0) cc_final: 0.7503 (t0) REVERT: A 74 TYR cc_start: 0.7885 (m-80) cc_final: 0.7611 (m-10) REVERT: A 208 ASP cc_start: 0.8239 (m-30) cc_final: 0.7760 (t70) REVERT: A 292 LYS cc_start: 0.8367 (pptt) cc_final: 0.8046 (mtmt) REVERT: B 1 MET cc_start: 0.8844 (mpp) cc_final: 0.8384 (ttt) REVERT: B 48 TYR cc_start: 0.8980 (m-80) cc_final: 0.8332 (m-80) REVERT: B 54 GLN cc_start: 0.8426 (pt0) cc_final: 0.7991 (pt0) REVERT: B 120 GLU cc_start: 0.8708 (pm20) cc_final: 0.8338 (tp30) REVERT: B 142 ASP cc_start: 0.9061 (t70) cc_final: 0.8712 (m-30) REVERT: B 234 TYR cc_start: 0.8866 (t80) cc_final: 0.8156 (t80) REVERT: B 252 MET cc_start: 0.8152 (tmm) cc_final: 0.7841 (tmm) REVERT: B 292 LYS cc_start: 0.8328 (pptt) cc_final: 0.8062 (mttt) REVERT: C 1 MET cc_start: 0.8638 (mpp) cc_final: 0.8189 (ttt) REVERT: C 58 ASP cc_start: 0.8268 (t70) cc_final: 0.8004 (t0) REVERT: C 74 TYR cc_start: 0.7754 (m-80) cc_final: 0.7409 (m-10) REVERT: C 148 GLU cc_start: 0.4894 (tt0) cc_final: 0.4585 (pt0) REVERT: D 1 MET cc_start: 0.8841 (mpp) cc_final: 0.8417 (ttt) REVERT: D 58 ASP cc_start: 0.8146 (t70) cc_final: 0.7929 (t0) REVERT: D 148 GLU cc_start: 0.5623 (tt0) cc_final: 0.5238 (tt0) REVERT: D 158 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8139 (mm110) REVERT: D 214 ARG cc_start: 0.8325 (mtm110) cc_final: 0.7969 (ttm110) REVERT: D 292 LYS cc_start: 0.8445 (pptt) cc_final: 0.8116 (mttp) REVERT: D 315 MET cc_start: 0.8571 (mtm) cc_final: 0.8320 (mtt) REVERT: E 1 MET cc_start: 0.8853 (mpp) cc_final: 0.8589 (ttt) REVERT: E 58 ASP cc_start: 0.8155 (t70) cc_final: 0.7867 (t0) REVERT: E 110 ARG cc_start: 0.7412 (mmp80) cc_final: 0.6958 (ttt180) REVERT: E 176 LEU cc_start: 0.8603 (tt) cc_final: 0.8177 (tt) REVERT: E 185 LEU cc_start: 0.8733 (mt) cc_final: 0.8496 (mt) REVERT: E 194 ASP cc_start: 0.6598 (t70) cc_final: 0.6138 (p0) REVERT: E 197 LEU cc_start: 0.8018 (mt) cc_final: 0.7680 (mt) REVERT: E 315 MET cc_start: 0.8508 (mtm) cc_final: 0.8219 (mtt) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2270 time to fit residues: 86.1473 Evaluate side-chains 204 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 30.0000 chunk 85 optimal weight: 0.9980 chunk 109 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 chunk 83 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 91 optimal weight: 0.9980 chunk 68 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 265 ASN D 78 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12890 Z= 0.187 Angle : 0.651 7.262 17495 Z= 0.342 Chirality : 0.043 0.188 2020 Planarity : 0.005 0.062 2220 Dihedral : 12.628 174.488 1860 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.19 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.20), residues: 1580 helix: -0.89 (0.21), residues: 570 sheet: 0.21 (0.28), residues: 360 loop : -1.94 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 72 HIS 0.004 0.001 HIS A 275 PHE 0.015 0.001 PHE C 302 TYR 0.029 0.002 TYR C 107 ARG 0.004 0.001 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8165 (t0) cc_final: 0.7486 (t0) REVERT: A 208 ASP cc_start: 0.8201 (m-30) cc_final: 0.7722 (t70) REVERT: A 292 LYS cc_start: 0.8432 (pptt) cc_final: 0.8111 (mtmt) REVERT: B 1 MET cc_start: 0.8887 (mpp) cc_final: 0.8494 (ttt) REVERT: B 48 TYR cc_start: 0.8959 (m-80) cc_final: 0.8369 (m-80) REVERT: B 106 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 142 ASP cc_start: 0.9016 (t70) cc_final: 0.8599 (m-30) REVERT: B 168 ILE cc_start: 0.8537 (mt) cc_final: 0.8247 (mm) REVERT: B 234 TYR cc_start: 0.8786 (t80) cc_final: 0.8051 (t80) REVERT: B 292 LYS cc_start: 0.8341 (pptt) cc_final: 0.8073 (mttt) REVERT: C 1 MET cc_start: 0.8660 (mpp) cc_final: 0.8255 (ttt) REVERT: C 58 ASP cc_start: 0.8214 (t70) cc_final: 0.7928 (t0) REVERT: C 223 ASP cc_start: 0.8852 (m-30) cc_final: 0.8389 (t0) REVERT: D 1 MET cc_start: 0.8744 (mpp) cc_final: 0.8372 (ttt) REVERT: D 74 TYR cc_start: 0.7428 (m-80) cc_final: 0.6916 (m-80) REVERT: D 120 GLU cc_start: 0.8335 (tp30) cc_final: 0.8133 (pt0) REVERT: D 148 GLU cc_start: 0.5504 (tt0) cc_final: 0.5064 (tt0) REVERT: D 154 TYR cc_start: 0.8558 (t80) cc_final: 0.8318 (t80) REVERT: D 214 ARG cc_start: 0.8353 (mtm110) cc_final: 0.7887 (ttm110) REVERT: D 292 LYS cc_start: 0.8466 (pptt) cc_final: 0.8137 (mttp) REVERT: E 1 MET cc_start: 0.8829 (mpp) cc_final: 0.8573 (ttt) REVERT: E 58 ASP cc_start: 0.8213 (t70) cc_final: 0.7954 (t0) REVERT: E 110 ARG cc_start: 0.7265 (mmp80) cc_final: 0.6800 (ttt180) REVERT: E 176 LEU cc_start: 0.8611 (tt) cc_final: 0.8169 (tt) REVERT: E 185 LEU cc_start: 0.8706 (mt) cc_final: 0.8475 (mt) REVERT: E 194 ASP cc_start: 0.6596 (t70) cc_final: 0.6153 (p0) REVERT: E 197 LEU cc_start: 0.8101 (mt) cc_final: 0.7840 (mt) REVERT: E 315 MET cc_start: 0.8399 (mtm) cc_final: 0.8155 (mtt) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2389 time to fit residues: 91.0819 Evaluate side-chains 201 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 29 optimal weight: 0.0670 chunk 28 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 overall best weight: 5.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 265 ASN D 78 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12890 Z= 0.203 Angle : 0.661 7.543 17495 Z= 0.347 Chirality : 0.043 0.197 2020 Planarity : 0.005 0.078 2220 Dihedral : 12.463 171.004 1860 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.87 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.20), residues: 1580 helix: -0.65 (0.22), residues: 540 sheet: 0.27 (0.28), residues: 360 loop : -1.99 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 72 HIS 0.007 0.001 HIS A 275 PHE 0.013 0.002 PHE E 138 TYR 0.027 0.002 TYR C 107 ARG 0.004 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8196 (t0) cc_final: 0.7530 (t0) REVERT: A 208 ASP cc_start: 0.8196 (m-30) cc_final: 0.7718 (t70) REVERT: A 230 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7411 (pttm) REVERT: A 252 MET cc_start: 0.7605 (tmm) cc_final: 0.7348 (tmm) REVERT: A 292 LYS cc_start: 0.8435 (pptt) cc_final: 0.8117 (mtmt) REVERT: B 48 TYR cc_start: 0.8948 (m-80) cc_final: 0.8372 (m-80) REVERT: B 54 GLN cc_start: 0.8486 (pt0) cc_final: 0.8012 (pt0) REVERT: B 142 ASP cc_start: 0.8958 (t70) cc_final: 0.8566 (m-30) REVERT: B 168 ILE cc_start: 0.8543 (mt) cc_final: 0.8218 (mm) REVERT: B 234 TYR cc_start: 0.8786 (t80) cc_final: 0.8112 (t80) REVERT: B 292 LYS cc_start: 0.8431 (pptt) cc_final: 0.8151 (mttt) REVERT: C 1 MET cc_start: 0.8674 (mpp) cc_final: 0.8289 (ttt) REVERT: C 58 ASP cc_start: 0.8097 (t70) cc_final: 0.7818 (t0) REVERT: C 106 GLU cc_start: 0.8240 (tp30) cc_final: 0.7989 (tp30) REVERT: C 223 ASP cc_start: 0.8882 (m-30) cc_final: 0.8396 (t0) REVERT: D 117 GLU cc_start: 0.8810 (tp30) cc_final: 0.8461 (tp30) REVERT: D 292 LYS cc_start: 0.8544 (pptt) cc_final: 0.8223 (mttp) REVERT: D 315 MET cc_start: 0.8594 (mtm) cc_final: 0.8350 (mtt) REVERT: E 34 ARG cc_start: 0.9009 (mtm180) cc_final: 0.8746 (mtt90) REVERT: E 58 ASP cc_start: 0.8263 (t70) cc_final: 0.8033 (t0) REVERT: E 110 ARG cc_start: 0.7392 (mmp80) cc_final: 0.6943 (ttt180) REVERT: E 176 LEU cc_start: 0.8558 (tt) cc_final: 0.8072 (tt) REVERT: E 185 LEU cc_start: 0.8959 (mt) cc_final: 0.8675 (mt) REVERT: E 194 ASP cc_start: 0.6594 (t70) cc_final: 0.6198 (p0) REVERT: E 197 LEU cc_start: 0.7971 (mt) cc_final: 0.7682 (mt) REVERT: E 229 ARG cc_start: 0.8490 (mtp-110) cc_final: 0.8032 (mtm180) REVERT: E 292 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8558 (mmtm) REVERT: E 315 MET cc_start: 0.8518 (mtm) cc_final: 0.8205 (mtt) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2370 time to fit residues: 89.9352 Evaluate side-chains 217 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.2980 chunk 130 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 60 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 30.0000 chunk 125 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 138 optimal weight: 0.0010 chunk 91 optimal weight: 0.9980 overall best weight: 1.2746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 265 ASN A 308 GLN B 26 HIS B 158 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.7034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12890 Z= 0.152 Angle : 0.640 8.354 17495 Z= 0.328 Chirality : 0.042 0.199 2020 Planarity : 0.004 0.065 2220 Dihedral : 12.005 165.547 1860 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.86 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.42 (0.21), residues: 1580 helix: -0.58 (0.22), residues: 540 sheet: 0.32 (0.28), residues: 360 loop : -1.93 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 72 HIS 0.005 0.001 HIS A 275 PHE 0.011 0.001 PHE C 138 TYR 0.019 0.001 TYR C 107 ARG 0.004 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.655 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 58 ASP cc_start: 0.8280 (t0) cc_final: 0.7738 (t0) REVERT: A 208 ASP cc_start: 0.8123 (m-30) cc_final: 0.7638 (t70) REVERT: A 223 ASP cc_start: 0.8749 (m-30) cc_final: 0.8541 (t0) REVERT: A 230 LYS cc_start: 0.7847 (mmtm) cc_final: 0.7199 (pttm) REVERT: A 252 MET cc_start: 0.7645 (tmm) cc_final: 0.7399 (tmm) REVERT: B 48 TYR cc_start: 0.8861 (m-80) cc_final: 0.8372 (m-80) REVERT: B 54 GLN cc_start: 0.8398 (pt0) cc_final: 0.7965 (pt0) REVERT: B 142 ASP cc_start: 0.8905 (t70) cc_final: 0.8481 (m-30) REVERT: B 146 MET cc_start: 0.6585 (mtp) cc_final: 0.6247 (mtm) REVERT: B 168 ILE cc_start: 0.8503 (mt) cc_final: 0.8194 (tp) REVERT: B 234 TYR cc_start: 0.8699 (t80) cc_final: 0.7988 (t80) REVERT: B 252 MET cc_start: 0.8160 (tmm) cc_final: 0.7542 (tmm) REVERT: B 292 LYS cc_start: 0.8465 (pptt) cc_final: 0.8178 (mptt) REVERT: C 58 ASP cc_start: 0.8289 (t70) cc_final: 0.8057 (t0) REVERT: C 106 GLU cc_start: 0.8319 (tp30) cc_final: 0.8037 (tp30) REVERT: C 148 GLU cc_start: 0.4690 (pt0) cc_final: 0.4470 (pm20) REVERT: C 162 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7418 (tp30) REVERT: D 106 GLU cc_start: 0.8263 (tp30) cc_final: 0.7963 (tp30) REVERT: D 214 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7843 (ttm110) REVERT: D 292 LYS cc_start: 0.8572 (pptt) cc_final: 0.8247 (mttp) REVERT: E 34 ARG cc_start: 0.8967 (mtm180) cc_final: 0.8637 (mtt90) REVERT: E 58 ASP cc_start: 0.8187 (t70) cc_final: 0.7966 (t0) REVERT: E 101 THR cc_start: 0.5347 (t) cc_final: 0.5145 (t) REVERT: E 110 ARG cc_start: 0.6938 (mmp80) cc_final: 0.6455 (ttt180) REVERT: E 176 LEU cc_start: 0.8538 (tt) cc_final: 0.8091 (tt) REVERT: E 194 ASP cc_start: 0.6521 (t70) cc_final: 0.6283 (p0) REVERT: E 197 LEU cc_start: 0.7937 (mt) cc_final: 0.7675 (mt) REVERT: E 229 ARG cc_start: 0.8389 (mtp-110) cc_final: 0.8088 (mtm180) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2343 time to fit residues: 95.4765 Evaluate side-chains 224 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 9.9990 chunk 89 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 142 optimal weight: 0.0050 chunk 122 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 chunk 97 optimal weight: 30.0000 overall best weight: 2.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12890 Z= 0.163 Angle : 0.642 6.883 17495 Z= 0.332 Chirality : 0.042 0.204 2020 Planarity : 0.005 0.060 2220 Dihedral : 11.822 164.538 1860 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.92 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.21), residues: 1580 helix: -0.56 (0.22), residues: 540 sheet: 0.29 (0.28), residues: 360 loop : -1.85 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 72 HIS 0.006 0.001 HIS B 26 PHE 0.014 0.001 PHE B 270 TYR 0.033 0.002 TYR E 154 ARG 0.005 0.001 ARG C 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8247 (t0) cc_final: 0.7960 (t0) REVERT: A 208 ASP cc_start: 0.8146 (m-30) cc_final: 0.7663 (t70) REVERT: A 223 ASP cc_start: 0.8770 (m-30) cc_final: 0.8529 (t0) REVERT: A 230 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7257 (pttm) REVERT: A 292 LYS cc_start: 0.8465 (pptt) cc_final: 0.8152 (mtmt) REVERT: B 34 ARG cc_start: 0.9172 (mtm110) cc_final: 0.8900 (mtm-85) REVERT: B 48 TYR cc_start: 0.8929 (m-80) cc_final: 0.8425 (m-80) REVERT: B 54 GLN cc_start: 0.8461 (pt0) cc_final: 0.7991 (pt0) REVERT: B 142 ASP cc_start: 0.8898 (t70) cc_final: 0.8503 (m-30) REVERT: B 154 TYR cc_start: 0.8448 (t80) cc_final: 0.8143 (t80) REVERT: B 168 ILE cc_start: 0.8548 (mt) cc_final: 0.8245 (tp) REVERT: B 229 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7671 (mtm180) REVERT: B 234 TYR cc_start: 0.8734 (t80) cc_final: 0.8165 (t80) REVERT: B 292 LYS cc_start: 0.8527 (pptt) cc_final: 0.8185 (mttt) REVERT: C 34 ARG cc_start: 0.9026 (mtt-85) cc_final: 0.8672 (mtt-85) REVERT: C 58 ASP cc_start: 0.8191 (t70) cc_final: 0.7943 (t0) REVERT: C 106 GLU cc_start: 0.8344 (tp30) cc_final: 0.8027 (tp30) REVERT: C 148 GLU cc_start: 0.4967 (pt0) cc_final: 0.4656 (pm20) REVERT: C 162 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7338 (tp30) REVERT: D 58 ASP cc_start: 0.8309 (t0) cc_final: 0.8081 (t0) REVERT: D 116 THR cc_start: 0.9265 (p) cc_final: 0.9005 (p) REVERT: D 117 GLU cc_start: 0.8818 (tp30) cc_final: 0.8494 (tp30) REVERT: D 292 LYS cc_start: 0.8640 (pptt) cc_final: 0.8336 (mttp) REVERT: E 34 ARG cc_start: 0.8962 (mtm180) cc_final: 0.8660 (mtt90) REVERT: E 58 ASP cc_start: 0.8234 (t70) cc_final: 0.8021 (t0) REVERT: E 110 ARG cc_start: 0.6940 (mmp80) cc_final: 0.6509 (ttt180) REVERT: E 176 LEU cc_start: 0.8481 (tt) cc_final: 0.8042 (tt) REVERT: E 194 ASP cc_start: 0.6558 (t70) cc_final: 0.6313 (p0) REVERT: E 229 ARG cc_start: 0.8359 (mtp-110) cc_final: 0.8008 (mtm180) REVERT: E 262 ARG cc_start: 0.8454 (ptp-170) cc_final: 0.8100 (ttt180) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2810 time to fit residues: 108.2174 Evaluate side-chains 221 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 265 ASN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075426 restraints weight = 49167.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.076960 restraints weight = 30450.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078072 restraints weight = 20927.213| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.7206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12890 Z= 0.204 Angle : 0.655 6.891 17495 Z= 0.342 Chirality : 0.043 0.205 2020 Planarity : 0.005 0.056 2220 Dihedral : 11.747 162.472 1860 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.06 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.21), residues: 1580 helix: -0.65 (0.22), residues: 540 sheet: 0.17 (0.28), residues: 365 loop : -1.83 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 72 HIS 0.005 0.001 HIS B 26 PHE 0.012 0.001 PHE B 138 TYR 0.033 0.002 TYR E 107 ARG 0.006 0.001 ARG E 238 =============================================================================== Job complete usr+sys time: 2647.54 seconds wall clock time: 48 minutes 56.34 seconds (2936.34 seconds total)