Starting phenix.real_space_refine on Wed Feb 14 20:46:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbk_22118/02_2024/6xbk_22118_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbk_22118/02_2024/6xbk_22118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbk_22118/02_2024/6xbk_22118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbk_22118/02_2024/6xbk_22118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbk_22118/02_2024/6xbk_22118_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbk_22118/02_2024/6xbk_22118_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6489 2.51 5 N 1735 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 71": "OE1" <-> "OE2" Residue "R ARG 74": "NH1" <-> "NH2" Residue "R ASP 97": "OD1" <-> "OD2" Residue "R GLU 100": "OE1" <-> "OE2" Residue "R ARG 113": "NH1" <-> "NH2" Residue "R TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R GLU 160": "OE1" <-> "OE2" Residue "R PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 181": "OE1" <-> "OE2" Residue "R PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 208": "OE1" <-> "OE2" Residue "R ASP 209": "OD1" <-> "OD2" Residue "R GLU 226": "OE1" <-> "OE2" Residue "R TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 290": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 296": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 482": "NH1" <-> "NH2" Residue "R ASP 506": "OD1" <-> "OD2" Residue "R GLU 508": "OE1" <-> "OE2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 1": "OD1" <-> "OD2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10214 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3674 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 21, 'TRANS': 446} Chain breaks: 1 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1736 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.95, per 1000 atoms: 0.58 Number of scatterers: 10214 At special positions: 0 Unit cell: (108.29, 119.952, 165.767, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1912 8.00 N 1735 7.00 C 6489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS R 64 " - pdb=" SG CYS R 178 " distance=2.03 Simple disulfide: pdb=" SG CYS R 70 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 496 " distance=2.03 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 154 " distance=2.03 Simple disulfide: pdb=" SG CYS R 147 " - pdb=" SG CYS R 169 " distance=2.03 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 213 " distance=2.03 Simple disulfide: pdb=" SG CYS R 217 " - pdb=" SG CYS R 295 " distance=2.03 Simple disulfide: pdb=" SG CYS R 314 " - pdb=" SG CYS R 390 " distance=2.03 Simple disulfide: pdb=" SG CYS R 490 " - pdb=" SG CYS R 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 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: 4.08 Conformation dependent library (CDL) restraints added in 1.9 seconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2414 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 32.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'R' and resid 99 through 113 removed outlier: 4.067A pdb=" N CYS R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU R 112 " --> pdb=" O LEU R 108 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG R 113 " --> pdb=" O TRP R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 5.028A pdb=" N VAL R 121 " --> pdb=" O ARG R 117 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 144 through 150 removed outlier: 3.787A pdb=" N THR R 150 " --> pdb=" O LEU R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 160 Processing helix chain 'R' and resid 224 through 254 Processing helix chain 'R' and resid 262 through 281 Processing helix chain 'R' and resid 289 through 294 Processing helix chain 'R' and resid 315 through 345 removed outlier: 3.596A pdb=" N VAL R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA R 345 " --> pdb=" O THR R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 377 Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 397 through 432 Proline residue: R 407 - end of helix removed outlier: 5.313A pdb=" N LYS R 430 " --> pdb=" O LEU R 426 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER R 431 " --> pdb=" O PHE R 427 " (cutoff:3.500A) Processing helix chain 'R' and resid 439 through 496 removed outlier: 3.916A pdb=" N LYS R 444 " --> pdb=" O LYS R 440 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG R 482 " --> pdb=" O ALA R 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 515 through 531 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.774A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.154A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing sheet with id= A, first strand: chain 'R' and resid 381 through 384 removed outlier: 3.517A pdb=" N ILE R 389 " --> pdb=" O ASP R 384 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.430A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.659A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 113 Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.893A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.584A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.786A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.486A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.331A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.524A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.779A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.815A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.366A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 143 through 146 415 hydrogen bonds defined for protein. 1194 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: 3.06 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1973 1.33 - 1.45: 2615 1.45 - 1.58: 5748 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 10443 Sorted by residual: bond pdb=" CD GLU A 8 " pdb=" OE1 GLU A 8 " ideal model delta sigma weight residual 1.249 1.345 -0.096 1.90e-02 2.77e+03 2.58e+01 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.30e-03 1.88e+04 2.24e+01 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.460 1.498 -0.038 8.60e-03 1.35e+04 1.91e+01 bond pdb=" N GLY B 185 " pdb=" CA GLY B 185 " ideal model delta sigma weight residual 1.443 1.479 -0.035 8.60e-03 1.35e+04 1.70e+01 bond pdb=" N VAL S 64 " pdb=" CA VAL S 64 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.09e-02 8.42e+03 1.52e+01 ... (remaining 10438 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.12: 212 106.12 - 113.23: 5295 113.23 - 120.34: 4839 120.34 - 127.45: 3727 127.45 - 134.56: 84 Bond angle restraints: 14157 Sorted by residual: angle pdb=" C TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta sigma weight residual 110.17 122.85 -12.68 1.97e+00 2.58e-01 4.14e+01 angle pdb=" C GLU R 194 " pdb=" N VAL R 195 " pdb=" CA VAL R 195 " ideal model delta sigma weight residual 120.33 125.11 -4.78 8.00e-01 1.56e+00 3.56e+01 angle pdb=" C THR R 170 " pdb=" CA THR R 170 " pdb=" CB THR R 170 " ideal model delta sigma weight residual 108.63 115.87 -7.24 1.54e+00 4.22e-01 2.21e+01 angle pdb=" C PHE R 526 " pdb=" N GLY R 527 " pdb=" CA GLY R 527 " ideal model delta sigma weight residual 119.98 125.01 -5.03 1.11e+00 8.12e-01 2.05e+01 angle pdb=" CA ALA B 28 " pdb=" C ALA B 28 " pdb=" O ALA B 28 " ideal model delta sigma weight residual 120.80 116.06 4.74 1.05e+00 9.07e-01 2.04e+01 ... (remaining 14152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 5934 25.09 - 50.18: 278 50.18 - 75.27: 19 75.27 - 100.35: 5 100.35 - 125.44: 2 Dihedral angle restraints: 6238 sinusoidal: 2482 harmonic: 3756 Sorted by residual: dihedral pdb=" CA GLU R 305 " pdb=" C GLU R 305 " pdb=" N PRO R 306 " pdb=" CA PRO R 306 " ideal model delta harmonic sigma weight residual -180.00 -54.56 -125.44 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual -180.00 -62.75 -117.25 0 5.00e+00 4.00e-02 5.50e+02 dihedral pdb=" CB CYS R 147 " pdb=" SG CYS R 147 " pdb=" SG CYS R 169 " pdb=" CB CYS R 169 " ideal model delta sinusoidal sigma weight residual -86.00 -170.68 84.68 1 1.00e+01 1.00e-02 8.71e+01 ... (remaining 6235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 844 0.064 - 0.128: 581 0.128 - 0.191: 145 0.191 - 0.255: 4 0.255 - 0.319: 2 Chirality restraints: 1576 Sorted by residual: chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C14 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C15 CLR R 701 " pdb=" C8 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1573 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU R 305 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO R 306 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO R 306 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO R 306 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 305 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C GLU R 305 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU R 305 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO R 306 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO S 224 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " -0.045 5.00e-02 4.00e+02 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 648 2.75 - 3.29: 10262 3.29 - 3.83: 15614 3.83 - 4.36: 20022 4.36 - 4.90: 34033 Nonbonded interactions: 80579 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.219 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR R 85 " pdb=" O MET R 131 " model vdw 2.319 2.440 nonbonded pdb=" O THR B 29 " pdb=" N GLN B 32 " model vdw 2.327 2.520 nonbonded pdb=" NH1 ARG S 168 " pdb=" O GLU S 210 " model vdw 2.329 2.520 ... (remaining 80574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.200 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.210 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.014 0.096 10443 Z= 0.908 Angle : 1.702 12.680 14157 Z= 1.259 Chirality : 0.079 0.319 1576 Planarity : 0.005 0.103 1804 Dihedral : 13.465 125.443 3785 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -3.09 (0.20), residues: 1286 helix: -0.92 (0.22), residues: 419 sheet: -2.40 (0.32), residues: 232 loop : -2.73 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 99 HIS 0.008 0.001 HIS R 340 PHE 0.022 0.002 PHE R 318 TYR 0.026 0.002 TYR S 103 ARG 0.011 0.001 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 1.209 Fit side-chains REVERT: R 119 TRP cc_start: 0.7799 (t60) cc_final: 0.7430 (t60) REVERT: R 230 MET cc_start: 0.7130 (tpp) cc_final: 0.6708 (tpp) REVERT: R 457 PHE cc_start: 0.7218 (t80) cc_final: 0.6925 (m-10) REVERT: R 491 GLN cc_start: 0.8429 (tp40) cc_final: 0.8090 (tt0) REVERT: R 525 MET cc_start: 0.7993 (ttt) cc_final: 0.7601 (ttt) REVERT: A 345 LYS cc_start: 0.7294 (tmmt) cc_final: 0.6930 (mtpp) REVERT: B 6 GLN cc_start: 0.7332 (pp30) cc_final: 0.7013 (pp30) REVERT: B 19 ARG cc_start: 0.7253 (tmm160) cc_final: 0.6680 (ttp-110) REVERT: B 42 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7176 (ttm-80) REVERT: B 44 GLN cc_start: 0.7451 (tt0) cc_final: 0.6631 (pp30) REVERT: B 46 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.7020 (mtp85) REVERT: B 99 TRP cc_start: 0.8300 (m100) cc_final: 0.8055 (m100) REVERT: B 127 LYS cc_start: 0.8369 (mmtm) cc_final: 0.7834 (mmtp) REVERT: B 175 GLN cc_start: 0.7844 (pt0) cc_final: 0.7393 (mm110) REVERT: B 215 GLU cc_start: 0.8541 (mp0) cc_final: 0.8124 (mp0) REVERT: B 217 MET cc_start: 0.7494 (ptp) cc_final: 0.7243 (ptt) REVERT: B 254 ASP cc_start: 0.7514 (t70) cc_final: 0.6969 (t0) REVERT: B 316 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7559 (p) REVERT: G 47 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7704 (mp0) REVERT: S 13 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8122 (mm-40) REVERT: S 46 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7064 (tt0) REVERT: S 62 ASP cc_start: 0.8051 (m-30) cc_final: 0.7831 (m-30) REVERT: S 113 GLN cc_start: 0.8461 (mm110) cc_final: 0.7891 (mm-40) REVERT: S 148 ARG cc_start: 0.7918 (ttp80) cc_final: 0.6923 (ttm-80) REVERT: S 180 MET cc_start: 0.8046 (ptm) cc_final: 0.7546 (ptm) REVERT: S 190 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7932 (mtm-85) REVERT: S 208 GLU cc_start: 0.8366 (pt0) cc_final: 0.8021 (pt0) REVERT: S 234 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7688 (tm-30) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.2611 time to fit residues: 71.9077 Evaluate side-chains 147 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 180 ASN R 340 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 119 ASN B 295 ASN S 82 GLN S 113 GLN S 130 GLN S 155 HIS S 174 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10443 Z= 0.184 Angle : 0.577 9.987 14157 Z= 0.294 Chirality : 0.042 0.213 1576 Planarity : 0.005 0.136 1804 Dihedral : 5.633 81.440 1478 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.95 % Favored : 96.73 % Rotamer: Outliers : 2.44 % Allowed : 9.50 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.55 (0.23), residues: 1286 helix: 1.30 (0.26), residues: 413 sheet: -2.22 (0.30), residues: 257 loop : -2.17 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 119 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.001 PHE R 474 TYR 0.023 0.001 TYR S 223 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 TRP cc_start: 0.7808 (t60) cc_final: 0.7469 (t60) REVERT: R 230 MET cc_start: 0.7159 (tpp) cc_final: 0.6832 (tpp) REVERT: R 457 PHE cc_start: 0.7310 (t80) cc_final: 0.6997 (m-10) REVERT: A 52 GLN cc_start: 0.8026 (tp40) cc_final: 0.7136 (mt0) REVERT: A 345 LYS cc_start: 0.7304 (tmmt) cc_final: 0.7007 (mtpp) REVERT: B 19 ARG cc_start: 0.7132 (tmm160) cc_final: 0.6619 (ttp-110) REVERT: B 42 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7338 (ttm-80) REVERT: B 44 GLN cc_start: 0.7519 (tt0) cc_final: 0.6661 (pp30) REVERT: B 46 ARG cc_start: 0.7320 (ttt-90) cc_final: 0.6895 (mtp85) REVERT: B 127 LYS cc_start: 0.8433 (mmtm) cc_final: 0.7995 (mmtp) REVERT: B 175 GLN cc_start: 0.7727 (pt0) cc_final: 0.7295 (mm110) REVERT: B 215 GLU cc_start: 0.8487 (mp0) cc_final: 0.8067 (mp0) REVERT: B 217 MET cc_start: 0.7470 (ptp) cc_final: 0.7200 (ptt) REVERT: B 254 ASP cc_start: 0.7455 (t70) cc_final: 0.6872 (t0) REVERT: B 267 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8229 (t0) REVERT: G 46 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8455 (mtmm) REVERT: G 47 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7562 (mp0) REVERT: G 58 GLU cc_start: 0.8203 (mp0) cc_final: 0.7877 (mp0) REVERT: S 13 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7873 (mm-40) REVERT: S 46 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6965 (tt0) REVERT: S 93 MET cc_start: 0.7391 (mtp) cc_final: 0.6965 (ttt) REVERT: S 148 ARG cc_start: 0.7941 (ttp80) cc_final: 0.6895 (ttm-80) REVERT: S 180 MET cc_start: 0.8111 (ptm) cc_final: 0.7568 (ptm) REVERT: S 208 GLU cc_start: 0.8482 (pt0) cc_final: 0.8249 (pt0) REVERT: S 219 GLN cc_start: 0.9227 (pp30) cc_final: 0.8391 (pp30) REVERT: S 234 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7560 (tm-30) outliers start: 27 outliers final: 17 residues processed: 181 average time/residue: 0.2620 time to fit residues: 64.2444 Evaluate side-chains 161 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 202 ASN R 476 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10443 Z= 0.210 Angle : 0.553 7.911 14157 Z= 0.283 Chirality : 0.042 0.202 1576 Planarity : 0.004 0.087 1804 Dihedral : 5.571 77.114 1477 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.43 % Favored : 95.26 % Rotamer: Outliers : 3.89 % Allowed : 10.59 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.23 (0.24), residues: 1286 helix: 1.52 (0.26), residues: 421 sheet: -2.05 (0.30), residues: 270 loop : -1.97 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 331 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE R 455 TYR 0.027 0.001 TYR S 223 ARG 0.003 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 TRP cc_start: 0.7810 (t60) cc_final: 0.7468 (t60) REVERT: R 230 MET cc_start: 0.7216 (tpp) cc_final: 0.6864 (tpp) REVERT: R 399 TYR cc_start: 0.7694 (m-80) cc_final: 0.7428 (m-80) REVERT: R 424 MET cc_start: 0.6399 (mmt) cc_final: 0.6028 (mtt) REVERT: R 457 PHE cc_start: 0.7291 (t80) cc_final: 0.7082 (m-10) REVERT: R 491 GLN cc_start: 0.8083 (tt0) cc_final: 0.7755 (tt0) REVERT: A 9 ASP cc_start: 0.8004 (t0) cc_final: 0.7702 (m-30) REVERT: A 52 GLN cc_start: 0.7884 (tp40) cc_final: 0.7086 (mt0) REVERT: A 197 LYS cc_start: 0.7757 (mttt) cc_final: 0.7325 (mtpp) REVERT: A 345 LYS cc_start: 0.7251 (tmmt) cc_final: 0.6933 (mtpp) REVERT: B 19 ARG cc_start: 0.7164 (tmm160) cc_final: 0.6642 (ttm110) REVERT: B 42 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7313 (ttm-80) REVERT: B 44 GLN cc_start: 0.7515 (tt0) cc_final: 0.6663 (pp30) REVERT: B 46 ARG cc_start: 0.7303 (ttt-90) cc_final: 0.7011 (mtp85) REVERT: B 127 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7996 (mmtp) REVERT: B 175 GLN cc_start: 0.7764 (pt0) cc_final: 0.7244 (mm110) REVERT: B 215 GLU cc_start: 0.8498 (mp0) cc_final: 0.8065 (mp0) REVERT: B 217 MET cc_start: 0.7462 (ptp) cc_final: 0.7202 (ptt) REVERT: B 254 ASP cc_start: 0.7407 (t70) cc_final: 0.6845 (t0) REVERT: G 13 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6782 (mtm-85) REVERT: G 46 LYS cc_start: 0.8915 (mtmm) cc_final: 0.8458 (mtmm) REVERT: G 47 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7686 (mp0) REVERT: G 58 GLU cc_start: 0.8256 (mp0) cc_final: 0.7901 (mp0) REVERT: S 13 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7962 (mm-40) REVERT: S 46 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6973 (tt0) REVERT: S 93 MET cc_start: 0.7388 (mtp) cc_final: 0.7039 (ttt) REVERT: S 113 GLN cc_start: 0.8492 (mm-40) cc_final: 0.7990 (mm-40) REVERT: S 148 ARG cc_start: 0.7929 (ttp80) cc_final: 0.6874 (ttm-80) REVERT: S 174 GLN cc_start: 0.8066 (pt0) cc_final: 0.7794 (pt0) REVERT: S 180 MET cc_start: 0.8126 (ptm) cc_final: 0.7595 (ptm) REVERT: S 208 GLU cc_start: 0.8467 (pt0) cc_final: 0.8130 (pt0) REVERT: S 219 GLN cc_start: 0.9128 (pp30) cc_final: 0.8280 (pp30) REVERT: S 234 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7962 (tm-30) outliers start: 43 outliers final: 31 residues processed: 176 average time/residue: 0.2535 time to fit residues: 60.6710 Evaluate side-chains 171 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 103 HIS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 476 ASN Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 12 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 0.2980 chunk 123 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 491 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10443 Z= 0.356 Angle : 0.617 11.058 14157 Z= 0.314 Chirality : 0.044 0.174 1576 Planarity : 0.005 0.089 1804 Dihedral : 5.842 76.591 1477 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 4.07 % Allowed : 12.04 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.30 (0.23), residues: 1286 helix: 1.39 (0.26), residues: 420 sheet: -2.04 (0.29), residues: 282 loop : -1.95 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.006 0.001 HIS A 188 PHE 0.016 0.002 PHE R 455 TYR 0.033 0.002 TYR S 223 ARG 0.004 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: R 119 TRP cc_start: 0.7818 (t60) cc_final: 0.7397 (t60) REVERT: R 230 MET cc_start: 0.7287 (tpp) cc_final: 0.6963 (tpp) REVERT: R 317 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7459 (tp) REVERT: R 424 MET cc_start: 0.6480 (mmt) cc_final: 0.6121 (mtt) REVERT: R 457 PHE cc_start: 0.7381 (t80) cc_final: 0.7123 (m-10) REVERT: A 9 ASP cc_start: 0.8116 (t0) cc_final: 0.7735 (m-30) REVERT: A 52 GLN cc_start: 0.7994 (tp40) cc_final: 0.7181 (mt0) REVERT: A 197 LYS cc_start: 0.7841 (mttt) cc_final: 0.7340 (mtpp) REVERT: A 345 LYS cc_start: 0.7273 (tmmt) cc_final: 0.6924 (mtpp) REVERT: B 19 ARG cc_start: 0.7176 (tmm160) cc_final: 0.6625 (ttp-110) REVERT: B 42 ARG cc_start: 0.7869 (ttt-90) cc_final: 0.7354 (ttm-80) REVERT: B 44 GLN cc_start: 0.7476 (tt0) cc_final: 0.6641 (pp30) REVERT: B 46 ARG cc_start: 0.7363 (ttt-90) cc_final: 0.7074 (mtp85) REVERT: B 127 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8118 (mmtp) REVERT: B 175 GLN cc_start: 0.7784 (pt0) cc_final: 0.7274 (mm110) REVERT: B 215 GLU cc_start: 0.8439 (mp0) cc_final: 0.8020 (mp0) REVERT: B 217 MET cc_start: 0.7543 (ptp) cc_final: 0.7245 (ptt) REVERT: B 254 ASP cc_start: 0.7541 (t70) cc_final: 0.7098 (t0) REVERT: B 292 PHE cc_start: 0.8672 (m-10) cc_final: 0.8421 (m-10) REVERT: G 13 ARG cc_start: 0.7363 (mtm-85) cc_final: 0.6726 (mtm-85) REVERT: G 47 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7638 (mp0) REVERT: G 58 GLU cc_start: 0.8294 (mp0) cc_final: 0.7878 (mp0) REVERT: S 7 SER cc_start: 0.8875 (t) cc_final: 0.8619 (p) REVERT: S 13 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7987 (mm-40) REVERT: S 46 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6934 (tt0) REVERT: S 113 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8055 (mm-40) REVERT: S 148 ARG cc_start: 0.7825 (ttp80) cc_final: 0.6778 (ttm-80) REVERT: S 180 MET cc_start: 0.8234 (ptm) cc_final: 0.7837 (ptm) REVERT: S 208 GLU cc_start: 0.8528 (pt0) cc_final: 0.8284 (pt0) REVERT: S 234 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7949 (tm-30) outliers start: 45 outliers final: 38 residues processed: 174 average time/residue: 0.2528 time to fit residues: 60.4698 Evaluate side-chains 181 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 103 HIS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 0.0870 chunk 1 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 0.2980 chunk 0 optimal weight: 50.0000 chunk 63 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10443 Z= 0.184 Angle : 0.534 8.349 14157 Z= 0.271 Chirality : 0.041 0.180 1576 Planarity : 0.004 0.080 1804 Dihedral : 5.486 72.836 1477 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.12 % Favored : 95.65 % Rotamer: Outliers : 4.34 % Allowed : 12.76 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.03 (0.24), residues: 1286 helix: 1.49 (0.26), residues: 426 sheet: -1.80 (0.30), residues: 274 loop : -1.77 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 331 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE R 455 TYR 0.029 0.001 TYR S 223 ARG 0.004 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 151 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: R 119 TRP cc_start: 0.7819 (t60) cc_final: 0.7440 (t60) REVERT: R 230 MET cc_start: 0.7289 (tpp) cc_final: 0.6904 (tpp) REVERT: R 317 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7417 (tp) REVERT: R 399 TYR cc_start: 0.7840 (m-80) cc_final: 0.7570 (m-80) REVERT: R 424 MET cc_start: 0.6308 (mmt) cc_final: 0.5993 (mtt) REVERT: R 457 PHE cc_start: 0.7275 (t80) cc_final: 0.7071 (m-10) REVERT: A 9 ASP cc_start: 0.8020 (t0) cc_final: 0.7680 (m-30) REVERT: A 52 GLN cc_start: 0.7952 (tp40) cc_final: 0.7255 (mt0) REVERT: A 197 LYS cc_start: 0.7720 (mttt) cc_final: 0.7336 (mttp) REVERT: A 345 LYS cc_start: 0.7196 (tmmt) cc_final: 0.6919 (mtpp) REVERT: B 19 ARG cc_start: 0.7171 (tmm160) cc_final: 0.6621 (ttm110) REVERT: B 42 ARG cc_start: 0.7843 (ttt-90) cc_final: 0.7358 (ttm-80) REVERT: B 44 GLN cc_start: 0.7472 (tt0) cc_final: 0.6674 (pp30) REVERT: B 46 ARG cc_start: 0.7353 (ttt-90) cc_final: 0.7090 (mtp85) REVERT: B 99 TRP cc_start: 0.8335 (m100) cc_final: 0.8048 (m100) REVERT: B 127 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8048 (mmtp) REVERT: B 175 GLN cc_start: 0.7773 (pt0) cc_final: 0.7255 (mm110) REVERT: B 215 GLU cc_start: 0.8478 (mp0) cc_final: 0.8058 (mp0) REVERT: B 217 MET cc_start: 0.7495 (ptp) cc_final: 0.7231 (ptt) REVERT: B 228 ASP cc_start: 0.7505 (m-30) cc_final: 0.7139 (p0) REVERT: B 254 ASP cc_start: 0.7478 (t70) cc_final: 0.7122 (t0) REVERT: G 13 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.6713 (mtm-85) REVERT: G 22 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7249 (tt0) REVERT: G 46 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8535 (mtmm) REVERT: G 47 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7616 (mp0) REVERT: G 48 ASP cc_start: 0.8516 (t0) cc_final: 0.8314 (t0) REVERT: G 58 GLU cc_start: 0.8328 (mp0) cc_final: 0.7916 (mp0) REVERT: S 7 SER cc_start: 0.8840 (t) cc_final: 0.8580 (p) REVERT: S 13 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7943 (mm-40) REVERT: S 46 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6873 (tt0) REVERT: S 93 MET cc_start: 0.7338 (mtp) cc_final: 0.7052 (ttt) REVERT: S 113 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8106 (mm-40) REVERT: S 148 ARG cc_start: 0.7783 (ttp80) cc_final: 0.6729 (ttm-80) REVERT: S 180 MET cc_start: 0.8146 (ptm) cc_final: 0.7734 (ptm) REVERT: S 208 GLU cc_start: 0.8430 (pt0) cc_final: 0.7917 (pm20) REVERT: S 234 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7898 (tm-30) outliers start: 48 outliers final: 38 residues processed: 181 average time/residue: 0.2506 time to fit residues: 62.4606 Evaluate side-chains 182 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 103 HIS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 375 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10443 Z= 0.361 Angle : 0.605 8.867 14157 Z= 0.309 Chirality : 0.043 0.171 1576 Planarity : 0.005 0.083 1804 Dihedral : 5.830 74.373 1477 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.13 % Favored : 94.63 % Rotamer: Outliers : 4.80 % Allowed : 13.48 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.12 (0.23), residues: 1286 helix: 1.36 (0.26), residues: 426 sheet: -1.69 (0.30), residues: 279 loop : -1.86 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.006 0.001 HIS A 188 PHE 0.013 0.001 PHE B 241 TYR 0.033 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 144 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 230 MET cc_start: 0.7333 (tpp) cc_final: 0.6987 (tpp) REVERT: R 317 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7467 (tp) REVERT: R 399 TYR cc_start: 0.7841 (m-80) cc_final: 0.7520 (m-80) REVERT: R 424 MET cc_start: 0.6499 (mmt) cc_final: 0.6123 (mtt) REVERT: R 457 PHE cc_start: 0.7333 (t80) cc_final: 0.7114 (m-10) REVERT: A 9 ASP cc_start: 0.8148 (t0) cc_final: 0.7746 (m-30) REVERT: A 52 GLN cc_start: 0.8004 (tp40) cc_final: 0.7297 (mt0) REVERT: A 197 LYS cc_start: 0.7817 (mttt) cc_final: 0.7390 (mttp) REVERT: A 345 LYS cc_start: 0.7218 (tmmt) cc_final: 0.6928 (mtpp) REVERT: B 19 ARG cc_start: 0.7174 (tmm160) cc_final: 0.6624 (ttp-110) REVERT: B 42 ARG cc_start: 0.7905 (ttt-90) cc_final: 0.7447 (ttm-80) REVERT: B 44 GLN cc_start: 0.7470 (tt0) cc_final: 0.6594 (pp30) REVERT: B 46 ARG cc_start: 0.7382 (ttt-90) cc_final: 0.7079 (mtp85) REVERT: B 127 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8177 (mmtp) REVERT: B 175 GLN cc_start: 0.7828 (pt0) cc_final: 0.7329 (mm110) REVERT: B 215 GLU cc_start: 0.8454 (mp0) cc_final: 0.8033 (mp0) REVERT: B 217 MET cc_start: 0.7584 (ptp) cc_final: 0.7300 (ptt) REVERT: B 228 ASP cc_start: 0.7685 (m-30) cc_final: 0.7307 (p0) REVERT: B 254 ASP cc_start: 0.7566 (t70) cc_final: 0.7190 (t0) REVERT: B 292 PHE cc_start: 0.8733 (m-10) cc_final: 0.8464 (m-10) REVERT: G 13 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6773 (mtm-85) REVERT: G 22 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7414 (tt0) REVERT: G 47 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7565 (mp0) REVERT: G 58 GLU cc_start: 0.8332 (mp0) cc_final: 0.8114 (mp0) REVERT: S 7 SER cc_start: 0.8867 (t) cc_final: 0.8628 (p) REVERT: S 13 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7979 (mm-40) REVERT: S 46 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6946 (tt0) REVERT: S 113 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8131 (mm-40) REVERT: S 141 GLU cc_start: 0.8523 (pt0) cc_final: 0.8301 (pt0) REVERT: S 148 ARG cc_start: 0.7800 (ttp80) cc_final: 0.6795 (ttm-80) REVERT: S 180 MET cc_start: 0.8229 (ptm) cc_final: 0.7809 (ptm) REVERT: S 208 GLU cc_start: 0.8520 (pt0) cc_final: 0.8296 (pt0) REVERT: S 234 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7919 (tm-30) outliers start: 53 outliers final: 49 residues processed: 178 average time/residue: 0.2448 time to fit residues: 60.1147 Evaluate side-chains 190 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 140 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 103 HIS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 0.0170 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10443 Z= 0.201 Angle : 0.538 8.061 14157 Z= 0.273 Chirality : 0.041 0.177 1576 Planarity : 0.004 0.079 1804 Dihedral : 5.575 72.566 1477 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.59 % Favored : 95.18 % Rotamer: Outliers : 4.71 % Allowed : 14.21 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1286 helix: 1.47 (0.26), residues: 428 sheet: -1.60 (0.31), residues: 264 loop : -1.73 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE R 455 TYR 0.027 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 143 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 230 MET cc_start: 0.7305 (tpp) cc_final: 0.6927 (tpp) REVERT: R 317 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7413 (tp) REVERT: R 399 TYR cc_start: 0.7826 (m-80) cc_final: 0.7496 (m-80) REVERT: R 424 MET cc_start: 0.6282 (mmt) cc_final: 0.5928 (mtt) REVERT: A 9 ASP cc_start: 0.8055 (t0) cc_final: 0.7690 (m-30) REVERT: A 52 GLN cc_start: 0.7989 (tp40) cc_final: 0.7303 (mt0) REVERT: A 197 LYS cc_start: 0.7769 (mttt) cc_final: 0.7368 (mttp) REVERT: A 345 LYS cc_start: 0.7185 (tmmt) cc_final: 0.6901 (mtpp) REVERT: B 19 ARG cc_start: 0.7138 (tmm160) cc_final: 0.6628 (ttp-110) REVERT: B 42 ARG cc_start: 0.7912 (ttt-90) cc_final: 0.7435 (ttm-80) REVERT: B 44 GLN cc_start: 0.7473 (tt0) cc_final: 0.6622 (pp30) REVERT: B 46 ARG cc_start: 0.7374 (ttt-90) cc_final: 0.7096 (mtp85) REVERT: B 127 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8086 (mmtp) REVERT: B 175 GLN cc_start: 0.7822 (pt0) cc_final: 0.7323 (mm110) REVERT: B 215 GLU cc_start: 0.8438 (mp0) cc_final: 0.8008 (mp0) REVERT: B 217 MET cc_start: 0.7538 (ptp) cc_final: 0.7247 (ptt) REVERT: B 218 CYS cc_start: 0.7992 (p) cc_final: 0.7623 (p) REVERT: B 228 ASP cc_start: 0.7568 (m-30) cc_final: 0.7200 (p0) REVERT: B 254 ASP cc_start: 0.7513 (t70) cc_final: 0.7244 (t0) REVERT: B 292 PHE cc_start: 0.8670 (m-10) cc_final: 0.8401 (m-10) REVERT: G 13 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.6735 (mtm-85) REVERT: G 22 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7419 (tt0) REVERT: G 46 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8560 (mtmm) REVERT: G 47 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7559 (mp0) REVERT: G 48 ASP cc_start: 0.8562 (t0) cc_final: 0.8356 (t0) REVERT: G 58 GLU cc_start: 0.8328 (mp0) cc_final: 0.8108 (mp0) REVERT: S 7 SER cc_start: 0.8854 (t) cc_final: 0.8595 (p) REVERT: S 13 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7961 (mm-40) REVERT: S 46 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6874 (tt0) REVERT: S 93 MET cc_start: 0.7339 (mtp) cc_final: 0.7036 (ttt) REVERT: S 113 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8155 (mm-40) REVERT: S 141 GLU cc_start: 0.8524 (pt0) cc_final: 0.8252 (pt0) REVERT: S 148 ARG cc_start: 0.7716 (ttp80) cc_final: 0.6682 (ttm-80) REVERT: S 180 MET cc_start: 0.8199 (ptm) cc_final: 0.7783 (ptm) REVERT: S 208 GLU cc_start: 0.8441 (pt0) cc_final: 0.7914 (pm20) REVERT: S 234 GLU cc_start: 0.8258 (tm-30) cc_final: 0.8011 (tm-30) outliers start: 52 outliers final: 45 residues processed: 179 average time/residue: 0.2407 time to fit residues: 59.3021 Evaluate side-chains 184 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 103 HIS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 375 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.0570 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.0000 chunk 96 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10443 Z= 0.294 Angle : 0.577 8.910 14157 Z= 0.293 Chirality : 0.042 0.172 1576 Planarity : 0.004 0.081 1804 Dihedral : 5.691 72.970 1477 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.21 % Favored : 94.56 % Rotamer: Outliers : 4.89 % Allowed : 14.39 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.00 (0.23), residues: 1286 helix: 1.42 (0.26), residues: 427 sheet: -1.67 (0.29), residues: 290 loop : -1.73 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.005 0.001 HIS A 188 PHE 0.012 0.001 PHE R 455 TYR 0.032 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 140 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 131 MET cc_start: 0.7174 (tpp) cc_final: 0.6960 (tpp) REVERT: R 230 MET cc_start: 0.7304 (tpp) cc_final: 0.6907 (tpp) REVERT: R 317 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7497 (tp) REVERT: R 380 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5796 (pm20) REVERT: R 399 TYR cc_start: 0.7816 (m-80) cc_final: 0.7488 (m-80) REVERT: R 424 MET cc_start: 0.6449 (mmt) cc_final: 0.6080 (mtt) REVERT: A 9 ASP cc_start: 0.8127 (t0) cc_final: 0.7734 (m-30) REVERT: A 52 GLN cc_start: 0.8005 (tp40) cc_final: 0.7309 (mt0) REVERT: A 53 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7362 (mtt) REVERT: A 197 LYS cc_start: 0.7810 (mttt) cc_final: 0.7396 (mttp) REVERT: A 345 LYS cc_start: 0.7204 (tmmt) cc_final: 0.6877 (mtpp) REVERT: B 19 ARG cc_start: 0.7121 (tmm160) cc_final: 0.6597 (ttp-110) REVERT: B 42 ARG cc_start: 0.7944 (ttt-90) cc_final: 0.7488 (ttm-80) REVERT: B 44 GLN cc_start: 0.7482 (tt0) cc_final: 0.6622 (pp30) REVERT: B 46 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.7132 (mtp85) REVERT: B 127 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8121 (mmtp) REVERT: B 175 GLN cc_start: 0.7813 (pt0) cc_final: 0.7325 (mm110) REVERT: B 215 GLU cc_start: 0.8443 (mp0) cc_final: 0.8024 (mp0) REVERT: B 217 MET cc_start: 0.7568 (ptp) cc_final: 0.7281 (ptt) REVERT: B 218 CYS cc_start: 0.8054 (p) cc_final: 0.7672 (p) REVERT: B 228 ASP cc_start: 0.7647 (m-30) cc_final: 0.7290 (p0) REVERT: B 254 ASP cc_start: 0.7565 (t70) cc_final: 0.7183 (t0) REVERT: B 292 PHE cc_start: 0.8723 (m-10) cc_final: 0.8485 (m-10) REVERT: G 13 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.6758 (mtm-85) REVERT: G 22 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7443 (tt0) REVERT: G 47 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7533 (mp0) REVERT: G 58 GLU cc_start: 0.8373 (mp0) cc_final: 0.8139 (mp0) REVERT: S 7 SER cc_start: 0.8865 (t) cc_final: 0.8621 (p) REVERT: S 13 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7955 (mm-40) REVERT: S 46 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6909 (tt0) REVERT: S 93 MET cc_start: 0.7413 (mtp) cc_final: 0.7107 (ttt) REVERT: S 113 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8168 (mm-40) REVERT: S 141 GLU cc_start: 0.8515 (pt0) cc_final: 0.8238 (pt0) REVERT: S 148 ARG cc_start: 0.7749 (ttp80) cc_final: 0.6749 (ttm-80) REVERT: S 180 MET cc_start: 0.8217 (ptm) cc_final: 0.7794 (ptm) REVERT: S 208 GLU cc_start: 0.8495 (pt0) cc_final: 0.8274 (pt0) REVERT: S 234 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8003 (tm-30) outliers start: 54 outliers final: 46 residues processed: 176 average time/residue: 0.2662 time to fit residues: 65.0342 Evaluate side-chains 187 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 138 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 103 HIS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 380 GLN Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10443 Z= 0.172 Angle : 0.534 8.028 14157 Z= 0.270 Chirality : 0.040 0.175 1576 Planarity : 0.004 0.078 1804 Dihedral : 5.449 71.280 1477 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.59 % Favored : 95.18 % Rotamer: Outliers : 4.71 % Allowed : 14.66 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1286 helix: 1.55 (0.26), residues: 428 sheet: -1.51 (0.30), residues: 278 loop : -1.62 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE R 455 TYR 0.027 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 142 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 230 MET cc_start: 0.7284 (tpp) cc_final: 0.6839 (tpp) REVERT: R 317 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7415 (tp) REVERT: R 399 TYR cc_start: 0.7799 (m-80) cc_final: 0.7565 (m-80) REVERT: R 424 MET cc_start: 0.6257 (mmt) cc_final: 0.5914 (mtt) REVERT: A 9 ASP cc_start: 0.8043 (t0) cc_final: 0.7610 (m-30) REVERT: A 52 GLN cc_start: 0.7989 (tp40) cc_final: 0.7391 (mt0) REVERT: A 53 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7505 (mtt) REVERT: A 187 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8148 (p) REVERT: A 197 LYS cc_start: 0.7771 (mttt) cc_final: 0.7381 (mttp) REVERT: A 345 LYS cc_start: 0.7168 (tmmt) cc_final: 0.6879 (mtpp) REVERT: B 19 ARG cc_start: 0.7128 (tmm160) cc_final: 0.6623 (ttp-110) REVERT: B 42 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.7424 (ttm-80) REVERT: B 44 GLN cc_start: 0.7524 (tt0) cc_final: 0.6676 (pp30) REVERT: B 46 ARG cc_start: 0.7352 (ttt-90) cc_final: 0.7073 (mtp85) REVERT: B 127 LYS cc_start: 0.8476 (mmtm) cc_final: 0.8055 (mmtp) REVERT: B 175 GLN cc_start: 0.7740 (pt0) cc_final: 0.7299 (mm110) REVERT: B 215 GLU cc_start: 0.8446 (mp0) cc_final: 0.8022 (mp0) REVERT: B 217 MET cc_start: 0.7529 (ptp) cc_final: 0.7251 (ptt) REVERT: B 218 CYS cc_start: 0.7973 (p) cc_final: 0.7563 (p) REVERT: B 228 ASP cc_start: 0.7520 (m-30) cc_final: 0.7150 (p0) REVERT: B 254 ASP cc_start: 0.7355 (t70) cc_final: 0.7089 (t0) REVERT: G 13 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.6742 (mtm-85) REVERT: G 22 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7421 (tt0) REVERT: G 47 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7549 (mp0) REVERT: G 58 GLU cc_start: 0.8367 (mp0) cc_final: 0.8145 (mp0) REVERT: S 7 SER cc_start: 0.8849 (t) cc_final: 0.8590 (p) REVERT: S 13 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7931 (mm-40) REVERT: S 46 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6826 (tt0) REVERT: S 93 MET cc_start: 0.7293 (mtp) cc_final: 0.7031 (ttt) REVERT: S 113 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8165 (mm-40) REVERT: S 141 GLU cc_start: 0.8523 (pt0) cc_final: 0.8249 (pt0) REVERT: S 148 ARG cc_start: 0.7665 (ttp80) cc_final: 0.6638 (ttm-80) REVERT: S 180 MET cc_start: 0.8143 (ptm) cc_final: 0.7709 (ptm) REVERT: S 208 GLU cc_start: 0.8430 (pt0) cc_final: 0.7926 (pm20) REVERT: S 234 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7995 (tm-30) outliers start: 52 outliers final: 45 residues processed: 178 average time/residue: 0.2397 time to fit residues: 59.1706 Evaluate side-chains 187 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 139 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 103 HIS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 375 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 433 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10443 Z= 0.366 Angle : 0.618 9.879 14157 Z= 0.314 Chirality : 0.043 0.164 1576 Planarity : 0.005 0.082 1804 Dihedral : 5.840 73.359 1477 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.68 % Favored : 94.01 % Rotamer: Outliers : 4.43 % Allowed : 14.84 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1286 helix: 1.43 (0.26), residues: 420 sheet: -1.63 (0.29), residues: 288 loop : -1.69 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.006 0.001 HIS A 188 PHE 0.013 0.001 PHE B 241 TYR 0.038 0.001 TYR S 223 ARG 0.005 0.000 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 140 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 131 MET cc_start: 0.7137 (tpp) cc_final: 0.6928 (tpp) REVERT: R 230 MET cc_start: 0.7313 (tpp) cc_final: 0.6904 (tpp) REVERT: R 317 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7528 (tp) REVERT: R 380 GLN cc_start: 0.6164 (OUTLIER) cc_final: 0.5881 (pm20) REVERT: R 424 MET cc_start: 0.6506 (mmt) cc_final: 0.6127 (mtt) REVERT: A 9 ASP cc_start: 0.8195 (t0) cc_final: 0.7766 (m-30) REVERT: A 52 GLN cc_start: 0.8002 (tp40) cc_final: 0.7306 (mt0) REVERT: A 197 LYS cc_start: 0.7827 (mttt) cc_final: 0.7408 (mttp) REVERT: A 286 CYS cc_start: 0.8918 (t) cc_final: 0.8637 (t) REVERT: A 345 LYS cc_start: 0.7243 (tmmt) cc_final: 0.6889 (mtpp) REVERT: B 19 ARG cc_start: 0.7127 (tmm160) cc_final: 0.6617 (ttp-110) REVERT: B 42 ARG cc_start: 0.7953 (ttt-90) cc_final: 0.7532 (ttm-80) REVERT: B 44 GLN cc_start: 0.7419 (tt0) cc_final: 0.6586 (pp30) REVERT: B 46 ARG cc_start: 0.7416 (ttt-90) cc_final: 0.7114 (mtp85) REVERT: B 127 LYS cc_start: 0.8611 (mmtm) cc_final: 0.8201 (mmtp) REVERT: B 175 GLN cc_start: 0.7813 (pt0) cc_final: 0.7326 (mm110) REVERT: B 215 GLU cc_start: 0.8441 (mp0) cc_final: 0.8033 (mp0) REVERT: B 217 MET cc_start: 0.7598 (ptp) cc_final: 0.7305 (ptt) REVERT: B 218 CYS cc_start: 0.8073 (p) cc_final: 0.7641 (p) REVERT: B 228 ASP cc_start: 0.7675 (m-30) cc_final: 0.7262 (p0) REVERT: B 254 ASP cc_start: 0.7559 (t70) cc_final: 0.7182 (t0) REVERT: B 292 PHE cc_start: 0.8760 (m-10) cc_final: 0.8514 (m-10) REVERT: G 13 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.6712 (mtm-85) REVERT: G 58 GLU cc_start: 0.8423 (mp0) cc_final: 0.8153 (mp0) REVERT: S 7 SER cc_start: 0.8873 (t) cc_final: 0.8628 (p) REVERT: S 13 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7961 (mm-40) REVERT: S 46 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6902 (tt0) REVERT: S 93 MET cc_start: 0.7460 (mtp) cc_final: 0.7109 (ttt) REVERT: S 113 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8179 (mm-40) REVERT: S 141 GLU cc_start: 0.8509 (pt0) cc_final: 0.8241 (pt0) REVERT: S 148 ARG cc_start: 0.7741 (ttp80) cc_final: 0.6768 (ttm-80) REVERT: S 180 MET cc_start: 0.8224 (ptm) cc_final: 0.7788 (ptm) REVERT: S 208 GLU cc_start: 0.8532 (pt0) cc_final: 0.8325 (pt0) REVERT: S 234 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7944 (tm-30) outliers start: 49 outliers final: 45 residues processed: 175 average time/residue: 0.2378 time to fit residues: 57.1749 Evaluate side-chains 186 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 103 HIS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 380 GLN Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 0.0670 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098678 restraints weight = 13582.699| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.64 r_work: 0.3104 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10443 Z= 0.180 Angle : 0.546 9.796 14157 Z= 0.276 Chirality : 0.041 0.174 1576 Planarity : 0.004 0.078 1804 Dihedral : 5.554 72.007 1477 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.35 % Favored : 95.41 % Rotamer: Outliers : 4.34 % Allowed : 15.20 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1286 helix: 1.57 (0.26), residues: 422 sheet: -1.45 (0.30), residues: 279 loop : -1.59 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 331 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.001 PHE R 403 TYR 0.026 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.35 seconds wall clock time: 52 minutes 15.33 seconds (3135.33 seconds total)