Starting phenix.real_space_refine on Mon Mar 11 17:04:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/03_2024/7vvl_32143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/03_2024/7vvl_32143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/03_2024/7vvl_32143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/03_2024/7vvl_32143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/03_2024/7vvl_32143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/03_2024/7vvl_32143.pdb" } resolution = 2.8 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= 0.001 sd= 0.010 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 53 5.16 5 C 5546 2.51 5 N 1523 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "P GLU 22": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 137": "OD1" <-> "OD2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 431": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8725 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1901 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2519 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 392 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 280 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2665 Classifications: {'peptide': 346, 'water': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 9, 'TRANS': 336, None: 1} Not linked: pdbres="TRP R 477 " pdbres="HOH R 501 " Chain breaks: 4 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 152 Time building chain proxies: 5.24, per 1000 atoms: 0.60 Number of scatterers: 8725 At special positions: 0 Unit cell: (128.374, 99.6003, 127.267, 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 53 16.00 O 1603 8.00 N 1523 7.00 C 5546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.07 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 41.8% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.787A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.520A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.632A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.568A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.163A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.537A pdb=" N TYR A 308 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.540A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 removed outlier: 3.511A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 11 through 24 removed outlier: 3.800A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.835A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 179 through 212 removed outlier: 4.196A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 removed outlier: 3.555A pdb=" N ILE R 222 " --> pdb=" O THR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.545A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 344 removed outlier: 3.541A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.648A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 359 removed outlier: 4.090A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.503A pdb=" N ASN R 374 " --> pdb=" O SER R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 400 No H-bonds generated for 'chain 'R' and resid 398 through 400' Processing helix chain 'R' and resid 401 through 413 removed outlier: 3.756A pdb=" N LEU R 406 " --> pdb=" O GLN R 402 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU R 407 " --> pdb=" O TYR R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.702A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.531A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 477 removed outlier: 3.692A pdb=" N LYS R 472 " --> pdb=" O ALA R 468 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER R 473 " --> pdb=" O GLU R 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.984A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.812A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.800A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.735A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.935A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.020A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.373A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.617A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.520A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.639A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 128 through 130 453 hydrogen bonds defined for protein. 1290 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: 2.45 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1424 1.30 - 1.43: 2492 1.43 - 1.56: 4915 1.56 - 1.69: 1 1.69 - 1.83: 78 Bond restraints: 8910 Sorted by residual: bond pdb=" CE1 HIS R 307 " pdb=" NE2 HIS R 307 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.79e+01 bond pdb=" C ARG R 150 " pdb=" O ARG R 150 " ideal model delta sigma weight residual 1.236 1.301 -0.064 1.26e-02 6.30e+03 2.61e+01 bond pdb=" C PRO A 351 " pdb=" O PRO A 351 " ideal model delta sigma weight residual 1.233 1.180 0.053 1.10e-02 8.26e+03 2.36e+01 bond pdb=" C ASN R 139 " pdb=" O ASN R 139 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.35e-02 5.49e+03 2.18e+01 bond pdb=" N VAL R 157 " pdb=" CA VAL R 157 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.11e+01 ... (remaining 8905 not shown) Histogram of bond angle deviations from ideal: 97.65 - 105.12: 119 105.12 - 112.59: 4218 112.59 - 120.06: 4269 120.06 - 127.53: 3385 127.53 - 135.00: 99 Bond angle restraints: 12090 Sorted by residual: angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 114.35 121.98 -7.63 1.25e+00 6.40e-01 3.72e+01 angle pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" O VAL A 224 " ideal model delta sigma weight residual 122.63 118.12 4.51 8.70e-01 1.32e+00 2.69e+01 angle pdb=" N GLU P 4 " pdb=" CA GLU P 4 " pdb=" C GLU P 4 " ideal model delta sigma weight residual 111.14 105.80 5.34 1.08e+00 8.57e-01 2.44e+01 angle pdb=" C GLU B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta sigma weight residual 119.94 125.41 -5.47 1.11e+00 8.12e-01 2.43e+01 angle pdb=" CB GLU A 312 " pdb=" CG GLU A 312 " pdb=" CD GLU A 312 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.70e+00 3.46e-01 2.14e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4523 17.64 - 35.27: 513 35.27 - 52.90: 167 52.90 - 70.54: 34 70.54 - 88.17: 18 Dihedral angle restraints: 5255 sinusoidal: 1978 harmonic: 3277 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -146.52 60.52 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.34 43.66 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CA THR A 359 " pdb=" C THR A 359 " pdb=" N GLU A 360 " pdb=" CA GLU A 360 " ideal model delta harmonic sigma weight residual 180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 752 0.068 - 0.136: 443 0.136 - 0.204: 138 0.204 - 0.272: 24 0.272 - 0.340: 4 Chirality restraints: 1361 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE R 135 " pdb=" CA ILE R 135 " pdb=" CG1 ILE R 135 " pdb=" CG2 ILE R 135 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA LEU B 318 " pdb=" N LEU B 318 " pdb=" C LEU B 318 " pdb=" CB LEU B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1358 not shown) Planarity restraints: 1545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 329 " -0.017 2.00e-02 2.50e+03 8.90e-03 1.98e+00 pdb=" CG TRP R 329 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP R 329 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP R 329 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 329 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 329 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 329 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 329 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 329 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.019 2.00e-02 2.50e+03 8.80e-03 1.94e+00 pdb=" CG TRP A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 134 " 0.004 2.00e-02 2.50e+03 8.46e-03 1.43e+00 pdb=" CG TYR R 134 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR R 134 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR R 134 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR R 134 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR R 134 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 134 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR R 134 " 0.001 2.00e-02 2.50e+03 ... (remaining 1542 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 561 2.74 - 3.28: 8583 3.28 - 3.82: 14112 3.82 - 4.36: 19286 4.36 - 4.90: 31185 Nonbonded interactions: 73727 Sorted by model distance: nonbonded pdb=" O SER R 356 " pdb=" OG SER R 356 " model vdw 2.204 2.440 nonbonded pdb=" O GLN R 438 " pdb=" ND1 HIS R 442 " model vdw 2.262 2.520 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.265 2.520 nonbonded pdb=" OG1 THR N 28 " pdb=" ND2 ASN N 31 " model vdw 2.289 2.520 nonbonded pdb=" NH1 ARG R 282 " pdb=" OD1 ASN R 348 " model vdw 2.303 2.520 ... (remaining 73722 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.080 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 26.420 Find NCS groups from input model: 0.260 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 0.066 8910 Z= 0.932 Angle : 1.688 9.035 12090 Z= 1.233 Chirality : 0.089 0.340 1361 Planarity : 0.003 0.012 1545 Dihedral : 17.696 88.173 3126 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 7.24 % Allowed : 19.15 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), residues: 1104 helix: -0.35 (0.23), residues: 426 sheet: 0.15 (0.37), residues: 206 loop : -1.03 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 271 HIS 0.006 0.001 HIS B 311 PHE 0.012 0.003 PHE R 378 TYR 0.016 0.003 TYR R 134 ARG 0.005 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 164 time to evaluate : 1.025 Fit side-chains REVERT: A 21 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6396 (pt0) REVERT: A 27 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6753 (tp30) REVERT: A 28 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6648 (ttmm) REVERT: A 49 ASP cc_start: 0.7293 (m-30) cc_final: 0.6698 (t0) REVERT: A 289 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: A 371 ASP cc_start: 0.8221 (t70) cc_final: 0.7731 (t0) REVERT: B 32 GLN cc_start: 0.5824 (pt0) cc_final: 0.5403 (tp40) REVERT: B 38 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6958 (p0) REVERT: B 59 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8578 (t80) REVERT: B 78 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8068 (tppp) REVERT: B 96 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7208 (ttm-80) REVERT: B 101 MET cc_start: 0.8775 (mtp) cc_final: 0.8350 (mtp) REVERT: B 137 ARG cc_start: 0.6834 (ttm110) cc_final: 0.6541 (ttm110) REVERT: B 138 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7801 (mt-10) REVERT: B 146 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8410 (tt) REVERT: B 156 GLN cc_start: 0.7526 (mt0) cc_final: 0.7310 (mt0) REVERT: B 175 GLN cc_start: 0.7620 (pt0) cc_final: 0.6779 (mm-40) REVERT: B 219 ARG cc_start: 0.7338 (mmm160) cc_final: 0.6731 (mmt-90) REVERT: B 220 GLN cc_start: 0.8781 (mt0) cc_final: 0.8335 (mt0) REVERT: B 270 ILE cc_start: 0.7915 (pt) cc_final: 0.7654 (pp) REVERT: B 277 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8552 (m) REVERT: B 301 LYS cc_start: 0.7584 (mtpp) cc_final: 0.7382 (mtpt) REVERT: G 44 HIS cc_start: 0.7802 (m90) cc_final: 0.7551 (m-70) REVERT: N 3 GLN cc_start: 0.6596 (tt0) cc_final: 0.6179 (tt0) REVERT: N 6 GLU cc_start: 0.6681 (mp0) cc_final: 0.6269 (mp0) REVERT: N 34 MET cc_start: 0.8507 (mmm) cc_final: 0.8299 (mmm) REVERT: N 39 GLN cc_start: 0.8408 (tt0) cc_final: 0.8012 (tt0) REVERT: N 53 GLN cc_start: 0.7523 (mp10) cc_final: 0.6943 (mp10) REVERT: N 76 LYS cc_start: 0.7068 (mppt) cc_final: 0.6567 (mttt) REVERT: N 83 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6351 (mtt) REVERT: N 95 TYR cc_start: 0.8530 (m-80) cc_final: 0.7898 (m-80) REVERT: N 104 THR cc_start: 0.8362 (p) cc_final: 0.8074 (p) REVERT: N 123 GLN cc_start: 0.6821 (mm-40) cc_final: 0.6464 (tp40) REVERT: R 36 GLU cc_start: 0.5469 (tt0) cc_final: 0.4930 (tp30) REVERT: R 133 ASP cc_start: 0.3942 (OUTLIER) cc_final: 0.3682 (t0) REVERT: R 182 GLU cc_start: 0.7675 (tt0) cc_final: 0.7447 (tt0) REVERT: R 186 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6590 (ttp-110) REVERT: R 189 MET cc_start: 0.7426 (tpt) cc_final: 0.7101 (tpp) REVERT: R 218 THR cc_start: 0.8351 (t) cc_final: 0.8144 (m) REVERT: R 220 ASN cc_start: 0.7906 (m-40) cc_final: 0.7698 (m-40) REVERT: R 224 MET cc_start: 0.6932 (mtt) cc_final: 0.6688 (mtm) REVERT: R 240 LYS cc_start: 0.6731 (ttpt) cc_final: 0.6371 (ttpp) REVERT: R 389 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7262 (mp) REVERT: R 405 LYS cc_start: 0.5768 (tptm) cc_final: 0.4801 (ttmm) REVERT: R 408 LYS cc_start: 0.7381 (tmtp) cc_final: 0.7118 (tptt) REVERT: R 441 MET cc_start: 0.8493 (mmt) cc_final: 0.8217 (mmt) REVERT: R 445 MET cc_start: 0.8425 (mmp) cc_final: 0.8184 (mmm) REVERT: R 469 GLU cc_start: 0.5882 (mt-10) cc_final: 0.5624 (mm-30) outliers start: 65 outliers final: 23 residues processed: 214 average time/residue: 1.2106 time to fit residues: 275.3734 Evaluate side-chains 174 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 186 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 341 SER Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 40.0000 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN G 59 ASN N 31 ASN P 16 ASN R 374 ASN R 402 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8910 Z= 0.201 Angle : 0.530 6.702 12090 Z= 0.293 Chirality : 0.042 0.160 1361 Planarity : 0.004 0.045 1545 Dihedral : 8.749 76.663 1291 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.24 % Allowed : 22.05 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1104 helix: 1.33 (0.24), residues: 444 sheet: -0.17 (0.34), residues: 216 loop : -0.63 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS R 420 PHE 0.018 0.002 PHE A 212 TYR 0.024 0.002 TYR R 191 ARG 0.003 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 145 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6446 (pt0) REVERT: A 27 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6572 (mm-30) REVERT: A 28 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6545 (mtpt) REVERT: A 49 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6641 (t0) REVERT: A 58 LYS cc_start: 0.6139 (mtpp) cc_final: 0.5875 (mmtp) REVERT: A 289 GLU cc_start: 0.7585 (pp20) cc_final: 0.7094 (tp30) REVERT: A 346 ARG cc_start: 0.7146 (mmm-85) cc_final: 0.6392 (mtm-85) REVERT: B 27 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.5729 (p0) REVERT: B 32 GLN cc_start: 0.5855 (pt0) cc_final: 0.5582 (tp40) REVERT: B 38 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7110 (p0) REVERT: B 66 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7337 (p0) REVERT: B 70 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 96 ARG cc_start: 0.7522 (mtm110) cc_final: 0.7211 (ttm-80) REVERT: B 101 MET cc_start: 0.8634 (mtp) cc_final: 0.8196 (mtp) REVERT: B 124 TYR cc_start: 0.8406 (m-80) cc_final: 0.7924 (m-80) REVERT: B 137 ARG cc_start: 0.7081 (ttm110) cc_final: 0.6808 (ttm110) REVERT: B 138 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 146 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8395 (tt) REVERT: B 156 GLN cc_start: 0.7386 (mt0) cc_final: 0.7116 (mt0) REVERT: B 220 GLN cc_start: 0.8163 (mt0) cc_final: 0.7945 (mt0) REVERT: N 3 GLN cc_start: 0.6509 (tt0) cc_final: 0.6069 (tt0) REVERT: N 39 GLN cc_start: 0.8349 (tt0) cc_final: 0.7961 (tt0) REVERT: N 53 GLN cc_start: 0.7319 (mp10) cc_final: 0.6655 (mp10) REVERT: N 80 TYR cc_start: 0.7787 (m-80) cc_final: 0.6330 (m-80) REVERT: N 83 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6734 (mtt) REVERT: N 104 THR cc_start: 0.8116 (p) cc_final: 0.7846 (p) REVERT: N 105 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6338 (mmm-85) REVERT: N 123 GLN cc_start: 0.6799 (mm-40) cc_final: 0.6568 (tp-100) REVERT: R 182 GLU cc_start: 0.7417 (tt0) cc_final: 0.7149 (tt0) REVERT: R 189 MET cc_start: 0.7249 (tpt) cc_final: 0.7003 (tpp) REVERT: R 218 THR cc_start: 0.8282 (t) cc_final: 0.7983 (m) REVERT: R 305 TYR cc_start: 0.8335 (t80) cc_final: 0.7641 (t80) REVERT: R 308 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7352 (p) REVERT: R 318 LYS cc_start: 0.5835 (mppt) cc_final: 0.5613 (mmtt) REVERT: R 404 ARG cc_start: 0.5911 (tmm160) cc_final: 0.5273 (tmt-80) outliers start: 56 outliers final: 27 residues processed: 182 average time/residue: 1.2584 time to fit residues: 243.2043 Evaluate side-chains 165 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 370 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 44 HIS P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8910 Z= 0.160 Angle : 0.465 5.538 12090 Z= 0.258 Chirality : 0.040 0.145 1361 Planarity : 0.003 0.049 1545 Dihedral : 7.205 72.825 1260 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.46 % Allowed : 23.27 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1104 helix: 1.89 (0.25), residues: 444 sheet: -0.05 (0.33), residues: 217 loop : -0.62 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.023 0.001 TYR R 191 ARG 0.003 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6563 (pt0) REVERT: A 27 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6504 (mm-30) REVERT: A 28 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6465 (mtpt) REVERT: A 49 ASP cc_start: 0.7245 (m-30) cc_final: 0.6586 (t0) REVERT: A 289 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6917 (tp30) REVERT: A 346 ARG cc_start: 0.7153 (mmm-85) cc_final: 0.5986 (mtt90) REVERT: B 27 ASP cc_start: 0.6217 (OUTLIER) cc_final: 0.5770 (p0) REVERT: B 38 ASP cc_start: 0.7378 (p0) cc_final: 0.7160 (p0) REVERT: B 70 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8404 (pp) REVERT: B 96 ARG cc_start: 0.7454 (mtm110) cc_final: 0.7120 (ttm-80) REVERT: B 101 MET cc_start: 0.8621 (mtp) cc_final: 0.8216 (mtp) REVERT: B 130 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.5471 (tt0) REVERT: B 137 ARG cc_start: 0.7085 (ttm110) cc_final: 0.6813 (ttm110) REVERT: B 138 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 146 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 156 GLN cc_start: 0.7292 (mt0) cc_final: 0.7050 (mt0) REVERT: N 3 GLN cc_start: 0.6471 (tt0) cc_final: 0.5826 (tt0) REVERT: N 39 GLN cc_start: 0.8365 (tt0) cc_final: 0.8035 (tt0) REVERT: N 53 GLN cc_start: 0.7272 (mp10) cc_final: 0.6649 (mp10) REVERT: N 80 TYR cc_start: 0.7679 (m-80) cc_final: 0.6054 (m-80) REVERT: N 86 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6926 (mp) REVERT: N 105 ARG cc_start: 0.6695 (ttt180) cc_final: 0.6344 (mmm-85) REVERT: N 123 GLN cc_start: 0.6864 (mm-40) cc_final: 0.6563 (tp-100) REVERT: R 34 LYS cc_start: 0.5534 (tttt) cc_final: 0.5193 (tttp) REVERT: R 45 GLN cc_start: 0.5907 (OUTLIER) cc_final: 0.4796 (tt0) REVERT: R 179 ARG cc_start: 0.5341 (mmt90) cc_final: 0.4441 (mmm-85) REVERT: R 218 THR cc_start: 0.8132 (t) cc_final: 0.7879 (m) REVERT: R 240 LYS cc_start: 0.6904 (ttpt) cc_final: 0.6506 (ttpp) REVERT: R 305 TYR cc_start: 0.8347 (t80) cc_final: 0.7700 (t80) REVERT: R 308 SER cc_start: 0.7656 (OUTLIER) cc_final: 0.7194 (p) REVERT: R 318 LYS cc_start: 0.5877 (mppt) cc_final: 0.5645 (mmtt) REVERT: R 404 ARG cc_start: 0.5936 (tmm160) cc_final: 0.5366 (tmt-80) outliers start: 49 outliers final: 24 residues processed: 174 average time/residue: 1.3360 time to fit residues: 246.3318 Evaluate side-chains 168 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 370 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 176 GLN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 44 HIS P 16 ASN R 223 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8910 Z= 0.204 Angle : 0.494 6.425 12090 Z= 0.269 Chirality : 0.041 0.155 1361 Planarity : 0.004 0.054 1545 Dihedral : 6.353 56.853 1249 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.57 % Allowed : 24.83 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1104 helix: 1.93 (0.25), residues: 444 sheet: -0.17 (0.33), residues: 219 loop : -0.64 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.002 PHE A 212 TYR 0.023 0.002 TYR R 191 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 135 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6561 (mm-30) REVERT: A 28 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6491 (mtpt) REVERT: A 58 LYS cc_start: 0.6123 (mtpp) cc_final: 0.5840 (mmtp) REVERT: A 289 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: A 346 ARG cc_start: 0.7104 (mmm-85) cc_final: 0.5970 (mtt90) REVERT: B 27 ASP cc_start: 0.6200 (OUTLIER) cc_final: 0.5764 (p0) REVERT: B 96 ARG cc_start: 0.7447 (mtm110) cc_final: 0.7115 (ttm-80) REVERT: B 101 MET cc_start: 0.8711 (mtp) cc_final: 0.8290 (mtp) REVERT: B 130 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5201 (tt0) REVERT: B 137 ARG cc_start: 0.7051 (ttm110) cc_final: 0.6763 (ttm110) REVERT: B 138 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 146 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8465 (tt) REVERT: B 156 GLN cc_start: 0.7389 (mt0) cc_final: 0.7102 (mt0) REVERT: N 3 GLN cc_start: 0.6480 (tt0) cc_final: 0.5988 (tt0) REVERT: N 39 GLN cc_start: 0.8391 (tt0) cc_final: 0.8060 (tt0) REVERT: N 53 GLN cc_start: 0.7256 (mp10) cc_final: 0.6571 (mp10) REVERT: N 80 TYR cc_start: 0.7666 (m-80) cc_final: 0.6175 (m-80) REVERT: N 86 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7040 (mp) REVERT: N 105 ARG cc_start: 0.6688 (ttt180) cc_final: 0.6403 (mmm-85) REVERT: N 123 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6682 (tp-100) REVERT: R 34 LYS cc_start: 0.5532 (tttt) cc_final: 0.5219 (tttp) REVERT: R 218 THR cc_start: 0.8103 (t) cc_final: 0.7857 (m) REVERT: R 305 TYR cc_start: 0.8404 (t80) cc_final: 0.7903 (t80) REVERT: R 308 SER cc_start: 0.7680 (OUTLIER) cc_final: 0.7204 (p) REVERT: R 318 LYS cc_start: 0.5867 (mppt) cc_final: 0.5606 (mmpt) REVERT: R 404 ARG cc_start: 0.6066 (tmm160) cc_final: 0.5478 (tmt-80) REVERT: R 469 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.5613 (mt-10) outliers start: 50 outliers final: 28 residues processed: 167 average time/residue: 1.3301 time to fit residues: 235.5740 Evaluate side-chains 166 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 0.0270 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 95 optimal weight: 0.0570 chunk 26 optimal weight: 10.0000 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 44 HIS P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8910 Z= 0.129 Angle : 0.441 7.226 12090 Z= 0.243 Chirality : 0.039 0.141 1361 Planarity : 0.003 0.053 1545 Dihedral : 5.359 57.355 1240 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.68 % Allowed : 26.28 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1104 helix: 2.17 (0.25), residues: 444 sheet: -0.14 (0.33), residues: 217 loop : -0.63 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.003 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 141 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6582 (pt0) REVERT: A 27 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6462 (mm-30) REVERT: A 28 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6564 (mtpt) REVERT: A 49 ASP cc_start: 0.7368 (m-30) cc_final: 0.6716 (t0) REVERT: A 60 MET cc_start: 0.6338 (mpt) cc_final: 0.6095 (mpt) REVERT: A 285 ASP cc_start: 0.7501 (t0) cc_final: 0.7210 (p0) REVERT: A 289 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6974 (tp30) REVERT: A 346 ARG cc_start: 0.7105 (mmm-85) cc_final: 0.5979 (mtt90) REVERT: B 27 ASP cc_start: 0.6186 (OUTLIER) cc_final: 0.5729 (p0) REVERT: B 96 ARG cc_start: 0.7418 (mtm110) cc_final: 0.7076 (ttm-80) REVERT: B 101 MET cc_start: 0.8621 (mtp) cc_final: 0.8242 (mtp) REVERT: B 124 TYR cc_start: 0.8353 (m-80) cc_final: 0.7789 (m-80) REVERT: B 130 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5237 (tt0) REVERT: B 137 ARG cc_start: 0.7069 (ttm110) cc_final: 0.6789 (ttm110) REVERT: B 138 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7582 (mt-10) REVERT: B 146 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8418 (tt) REVERT: B 156 GLN cc_start: 0.7289 (mt0) cc_final: 0.7004 (mt0) REVERT: B 201 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8787 (p) REVERT: G 62 ARG cc_start: 0.3616 (OUTLIER) cc_final: 0.3299 (ppt170) REVERT: N 3 GLN cc_start: 0.6477 (tt0) cc_final: 0.5978 (tt0) REVERT: N 39 GLN cc_start: 0.8391 (tt0) cc_final: 0.8051 (tt0) REVERT: N 46 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7670 (mt-10) REVERT: N 53 GLN cc_start: 0.7345 (mp10) cc_final: 0.6652 (mp10) REVERT: N 80 TYR cc_start: 0.7613 (m-80) cc_final: 0.5914 (m-80) REVERT: N 105 ARG cc_start: 0.6742 (ttt180) cc_final: 0.6211 (ttp-170) REVERT: R 34 LYS cc_start: 0.5617 (tttt) cc_final: 0.5326 (tttp) REVERT: R 218 THR cc_start: 0.8014 (t) cc_final: 0.7802 (m) REVERT: R 305 TYR cc_start: 0.8281 (t80) cc_final: 0.7659 (t80) REVERT: R 317 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5957 (mp0) REVERT: R 318 LYS cc_start: 0.6000 (mppt) cc_final: 0.5743 (mmpt) REVERT: R 390 ARG cc_start: 0.7046 (ttp80) cc_final: 0.6830 (ttp-110) REVERT: R 404 ARG cc_start: 0.6045 (tmm160) cc_final: 0.5542 (tmt-80) REVERT: R 469 GLU cc_start: 0.5772 (OUTLIER) cc_final: 0.5456 (mm-30) outliers start: 42 outliers final: 21 residues processed: 170 average time/residue: 1.3773 time to fit residues: 247.4758 Evaluate side-chains 162 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 359 LYS Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8910 Z= 0.207 Angle : 0.490 8.357 12090 Z= 0.266 Chirality : 0.041 0.158 1361 Planarity : 0.004 0.055 1545 Dihedral : 5.263 56.411 1236 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.57 % Allowed : 24.61 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1104 helix: 2.10 (0.25), residues: 439 sheet: -0.10 (0.34), residues: 217 loop : -0.62 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.016 0.002 PHE A 212 TYR 0.023 0.002 TYR R 191 ARG 0.003 0.000 ARG R 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 133 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6639 (tm-30) REVERT: A 27 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6507 (mm-30) REVERT: A 28 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6549 (mtpt) REVERT: A 273 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7609 (ptm160) REVERT: A 289 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: B 27 ASP cc_start: 0.6181 (OUTLIER) cc_final: 0.5715 (p0) REVERT: B 96 ARG cc_start: 0.7400 (mtm110) cc_final: 0.7124 (ttm-80) REVERT: B 101 MET cc_start: 0.8685 (mtp) cc_final: 0.8288 (mtp) REVERT: B 124 TYR cc_start: 0.8346 (m-80) cc_final: 0.7782 (m-80) REVERT: B 130 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.5229 (tt0) REVERT: B 137 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6818 (ttm110) REVERT: B 138 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 156 GLN cc_start: 0.7390 (mt0) cc_final: 0.7158 (mt0) REVERT: B 201 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8771 (p) REVERT: G 62 ARG cc_start: 0.3875 (OUTLIER) cc_final: 0.3507 (ppt170) REVERT: N 3 GLN cc_start: 0.6475 (tt0) cc_final: 0.5945 (tt0) REVERT: N 6 GLU cc_start: 0.6402 (mp0) cc_final: 0.6191 (mp0) REVERT: N 39 GLN cc_start: 0.8418 (tt0) cc_final: 0.8107 (tt0) REVERT: N 46 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7717 (mt-10) REVERT: N 53 GLN cc_start: 0.7306 (mp10) cc_final: 0.6642 (mp10) REVERT: N 80 TYR cc_start: 0.7617 (m-80) cc_final: 0.6058 (m-80) REVERT: N 105 ARG cc_start: 0.6831 (ttt180) cc_final: 0.6476 (mmm-85) REVERT: R 218 THR cc_start: 0.8027 (t) cc_final: 0.7794 (m) REVERT: R 305 TYR cc_start: 0.8391 (t80) cc_final: 0.7920 (t80) REVERT: R 308 SER cc_start: 0.7690 (OUTLIER) cc_final: 0.7237 (p) REVERT: R 317 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.6025 (mp0) REVERT: R 318 LYS cc_start: 0.6147 (mppt) cc_final: 0.5826 (mmpt) REVERT: R 390 ARG cc_start: 0.7054 (ttp80) cc_final: 0.6834 (ttp-110) REVERT: R 404 ARG cc_start: 0.6141 (tmm160) cc_final: 0.5634 (tmt-80) REVERT: R 457 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6317 (mt) REVERT: R 469 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.5380 (mt-10) outliers start: 59 outliers final: 28 residues processed: 173 average time/residue: 1.3726 time to fit residues: 251.2147 Evaluate side-chains 172 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 19 GLU Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 359 LYS Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 380 GLN B 142 HIS B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN P 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8910 Z= 0.359 Angle : 0.595 8.770 12090 Z= 0.321 Chirality : 0.045 0.178 1361 Planarity : 0.005 0.059 1545 Dihedral : 5.543 55.851 1234 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.90 % Allowed : 24.28 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1104 helix: 1.56 (0.25), residues: 439 sheet: -0.39 (0.33), residues: 220 loop : -0.75 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.002 PHE A 212 TYR 0.023 0.002 TYR R 191 ARG 0.004 0.001 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 139 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: A 27 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6583 (mm-30) REVERT: A 28 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6665 (mtpt) REVERT: A 58 LYS cc_start: 0.6118 (mtpp) cc_final: 0.5836 (mmtp) REVERT: A 60 MET cc_start: 0.6347 (mpt) cc_final: 0.6051 (mpt) REVERT: A 289 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7002 (tp30) REVERT: B 27 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5772 (p0) REVERT: B 101 MET cc_start: 0.8630 (mtp) cc_final: 0.8264 (mtp) REVERT: B 124 TYR cc_start: 0.8377 (m-80) cc_final: 0.7811 (m-80) REVERT: B 130 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5169 (tt0) REVERT: B 137 ARG cc_start: 0.6988 (ttm110) cc_final: 0.6754 (ttm110) REVERT: B 138 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 156 GLN cc_start: 0.7420 (mt0) cc_final: 0.7195 (mt0) REVERT: B 175 GLN cc_start: 0.7561 (pt0) cc_final: 0.6831 (mt0) REVERT: B 201 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8680 (p) REVERT: G 62 ARG cc_start: 0.3850 (OUTLIER) cc_final: 0.3499 (ppt170) REVERT: N 3 GLN cc_start: 0.6468 (tt0) cc_final: 0.5940 (tt0) REVERT: N 6 GLU cc_start: 0.6415 (mp0) cc_final: 0.6113 (mp0) REVERT: N 39 GLN cc_start: 0.8438 (tt0) cc_final: 0.7898 (tt0) REVERT: N 53 GLN cc_start: 0.7212 (mp10) cc_final: 0.6543 (mp10) REVERT: N 120 GLN cc_start: 0.6554 (mm-40) cc_final: 0.6243 (mm110) REVERT: R 34 LYS cc_start: 0.5466 (tttt) cc_final: 0.5170 (tttp) REVERT: R 179 ARG cc_start: 0.5660 (mmt90) cc_final: 0.4827 (mmm-85) REVERT: R 212 PHE cc_start: 0.5891 (m-80) cc_final: 0.5527 (m-10) REVERT: R 218 THR cc_start: 0.8057 (t) cc_final: 0.7778 (m) REVERT: R 305 TYR cc_start: 0.8437 (t80) cc_final: 0.8171 (t80) REVERT: R 317 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: R 318 LYS cc_start: 0.6117 (mppt) cc_final: 0.5770 (mmtt) REVERT: R 404 ARG cc_start: 0.6146 (tmm160) cc_final: 0.5645 (tmt-80) REVERT: R 457 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6329 (mm) REVERT: R 469 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5711 (mt-10) outliers start: 62 outliers final: 33 residues processed: 181 average time/residue: 1.3449 time to fit residues: 258.8103 Evaluate side-chains 178 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 72 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 92 optimal weight: 0.9980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 142 HIS B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8910 Z= 0.130 Angle : 0.458 9.418 12090 Z= 0.250 Chirality : 0.040 0.140 1361 Planarity : 0.004 0.055 1545 Dihedral : 4.947 57.704 1234 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.68 % Allowed : 26.39 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1104 helix: 2.18 (0.26), residues: 433 sheet: -0.23 (0.33), residues: 215 loop : -0.61 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.006 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6597 (tm-30) REVERT: A 27 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6504 (mm-30) REVERT: A 28 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6505 (mtpt) REVERT: A 60 MET cc_start: 0.6404 (mpt) cc_final: 0.6165 (mpt) REVERT: A 285 ASP cc_start: 0.7521 (t0) cc_final: 0.7281 (p0) REVERT: A 289 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6881 (tp30) REVERT: A 346 ARG cc_start: 0.7148 (mmm-85) cc_final: 0.6001 (mtt90) REVERT: B 27 ASP cc_start: 0.6209 (OUTLIER) cc_final: 0.5691 (p0) REVERT: B 32 GLN cc_start: 0.6193 (tp-100) cc_final: 0.5674 (tm-30) REVERT: B 101 MET cc_start: 0.8713 (mtp) cc_final: 0.8345 (mtp) REVERT: B 124 TYR cc_start: 0.8322 (m-80) cc_final: 0.7777 (m-80) REVERT: B 130 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.5221 (tt0) REVERT: B 137 ARG cc_start: 0.7036 (ttm110) cc_final: 0.6606 (ttm110) REVERT: B 138 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 156 GLN cc_start: 0.7299 (mt0) cc_final: 0.7066 (mt0) REVERT: B 175 GLN cc_start: 0.7580 (pt0) cc_final: 0.6816 (mt0) REVERT: G 62 ARG cc_start: 0.3919 (OUTLIER) cc_final: 0.3508 (ppt170) REVERT: N 3 GLN cc_start: 0.6353 (tt0) cc_final: 0.5843 (tt0) REVERT: N 6 GLU cc_start: 0.6386 (mp0) cc_final: 0.6011 (mp0) REVERT: N 39 GLN cc_start: 0.8407 (tt0) cc_final: 0.8106 (tt0) REVERT: N 53 GLN cc_start: 0.7281 (mp10) cc_final: 0.6637 (mp10) REVERT: N 78 THR cc_start: 0.7182 (m) cc_final: 0.6835 (p) REVERT: N 105 ARG cc_start: 0.6666 (ttt180) cc_final: 0.6210 (ttp-170) REVERT: N 120 GLN cc_start: 0.6505 (mm-40) cc_final: 0.6158 (mm110) REVERT: P 25 ARG cc_start: 0.5912 (ttp-110) cc_final: 0.5700 (ttp-110) REVERT: R 34 LYS cc_start: 0.5498 (tttt) cc_final: 0.5229 (tttp) REVERT: R 179 ARG cc_start: 0.5765 (mmt90) cc_final: 0.4929 (mmm-85) REVERT: R 305 TYR cc_start: 0.8292 (t80) cc_final: 0.7712 (t80) REVERT: R 308 SER cc_start: 0.7673 (OUTLIER) cc_final: 0.7236 (p) REVERT: R 318 LYS cc_start: 0.6249 (mppt) cc_final: 0.5903 (mmpt) REVERT: R 390 ARG cc_start: 0.6994 (ttp80) cc_final: 0.6773 (ttp-110) REVERT: R 404 ARG cc_start: 0.6097 (tmm160) cc_final: 0.5631 (tmt-80) REVERT: R 457 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6195 (mm) REVERT: R 469 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5280 (mm-30) outliers start: 42 outliers final: 18 residues processed: 165 average time/residue: 1.4219 time to fit residues: 247.7588 Evaluate side-chains 159 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 50.0000 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8910 Z= 0.214 Angle : 0.508 10.871 12090 Z= 0.273 Chirality : 0.041 0.156 1361 Planarity : 0.004 0.056 1545 Dihedral : 5.042 56.752 1234 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.23 % Allowed : 27.28 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1104 helix: 2.01 (0.25), residues: 439 sheet: -0.31 (0.33), residues: 218 loop : -0.60 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.002 PHE A 212 TYR 0.022 0.002 TYR R 191 ARG 0.006 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6593 (tm-30) REVERT: A 27 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6580 (mm-30) REVERT: A 28 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6555 (mtpt) REVERT: A 60 MET cc_start: 0.6306 (mpt) cc_final: 0.6039 (mpt) REVERT: A 289 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: B 27 ASP cc_start: 0.6202 (OUTLIER) cc_final: 0.5716 (p0) REVERT: B 32 GLN cc_start: 0.6062 (tp-100) cc_final: 0.5561 (tm-30) REVERT: B 101 MET cc_start: 0.8702 (mtp) cc_final: 0.8373 (mtp) REVERT: B 124 TYR cc_start: 0.8330 (m-80) cc_final: 0.7765 (m-80) REVERT: B 130 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5209 (tt0) REVERT: B 137 ARG cc_start: 0.6994 (ttm110) cc_final: 0.6753 (ttm110) REVERT: B 138 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 156 GLN cc_start: 0.7389 (mt0) cc_final: 0.7156 (mt0) REVERT: B 175 GLN cc_start: 0.7690 (pt0) cc_final: 0.6923 (mt0) REVERT: G 62 ARG cc_start: 0.3603 (OUTLIER) cc_final: 0.3241 (ppt170) REVERT: N 3 GLN cc_start: 0.6437 (tt0) cc_final: 0.5916 (tt0) REVERT: N 6 GLU cc_start: 0.6414 (mp0) cc_final: 0.6155 (mp0) REVERT: N 39 GLN cc_start: 0.8432 (tt0) cc_final: 0.8124 (tt0) REVERT: N 53 GLN cc_start: 0.7353 (mp10) cc_final: 0.6701 (mp10) REVERT: N 105 ARG cc_start: 0.6780 (ttt180) cc_final: 0.6421 (mmm-85) REVERT: N 120 GLN cc_start: 0.6548 (mm-40) cc_final: 0.6201 (mm110) REVERT: P 25 ARG cc_start: 0.5982 (ttp-110) cc_final: 0.5766 (ttp-110) REVERT: R 34 LYS cc_start: 0.5437 (tttt) cc_final: 0.5188 (tttp) REVERT: R 179 ARG cc_start: 0.5566 (mmt90) cc_final: 0.4789 (mmm-85) REVERT: R 212 PHE cc_start: 0.6022 (m-80) cc_final: 0.5386 (m-10) REVERT: R 305 TYR cc_start: 0.8384 (t80) cc_final: 0.7965 (t80) REVERT: R 308 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.7241 (p) REVERT: R 404 ARG cc_start: 0.6232 (tmm160) cc_final: 0.5747 (tmt-80) REVERT: R 457 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6224 (mm) REVERT: R 469 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5391 (mm-30) outliers start: 38 outliers final: 22 residues processed: 163 average time/residue: 1.4237 time to fit residues: 245.1215 Evaluate side-chains 164 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 359 LYS Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.0770 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8910 Z= 0.165 Angle : 0.485 11.232 12090 Z= 0.261 Chirality : 0.040 0.149 1361 Planarity : 0.004 0.056 1545 Dihedral : 4.901 57.050 1234 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.12 % Allowed : 27.51 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1104 helix: 2.18 (0.25), residues: 433 sheet: -0.28 (0.33), residues: 216 loop : -0.58 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG R 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6611 (tm-30) REVERT: A 27 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6562 (mm-30) REVERT: A 28 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6488 (mtpt) REVERT: A 49 ASP cc_start: 0.7105 (m-30) cc_final: 0.6504 (t0) REVERT: A 60 MET cc_start: 0.6288 (mpt) cc_final: 0.6059 (mpt) REVERT: A 285 ASP cc_start: 0.7539 (t0) cc_final: 0.7274 (p0) REVERT: A 289 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: A 346 ARG cc_start: 0.7159 (mmm-85) cc_final: 0.6012 (mtt90) REVERT: B 27 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5698 (p0) REVERT: B 32 GLN cc_start: 0.5963 (tp-100) cc_final: 0.5544 (tm-30) REVERT: B 101 MET cc_start: 0.8700 (mtp) cc_final: 0.8302 (mtp) REVERT: B 124 TYR cc_start: 0.8329 (m-80) cc_final: 0.7759 (m-80) REVERT: B 130 GLU cc_start: 0.5745 (OUTLIER) cc_final: 0.5224 (tt0) REVERT: B 137 ARG cc_start: 0.7010 (ttm110) cc_final: 0.6665 (tpp80) REVERT: B 138 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7690 (mt-10) REVERT: B 156 GLN cc_start: 0.7374 (mt0) cc_final: 0.7137 (mt0) REVERT: B 175 GLN cc_start: 0.7658 (pt0) cc_final: 0.6920 (mt0) REVERT: G 62 ARG cc_start: 0.3575 (OUTLIER) cc_final: 0.3212 (ppt170) REVERT: N 3 GLN cc_start: 0.6282 (tt0) cc_final: 0.5768 (tt0) REVERT: N 6 GLU cc_start: 0.6408 (mp0) cc_final: 0.6161 (mp0) REVERT: N 39 GLN cc_start: 0.8425 (tt0) cc_final: 0.8137 (tt0) REVERT: N 53 GLN cc_start: 0.7333 (mp10) cc_final: 0.6691 (mp10) REVERT: N 78 THR cc_start: 0.7340 (m) cc_final: 0.7013 (p) REVERT: N 105 ARG cc_start: 0.6757 (ttt180) cc_final: 0.6429 (mmm-85) REVERT: N 120 GLN cc_start: 0.6516 (mm-40) cc_final: 0.6161 (mm110) REVERT: N 123 GLN cc_start: 0.7069 (tp40) cc_final: 0.6421 (tm-30) REVERT: P 25 ARG cc_start: 0.5976 (ttp-110) cc_final: 0.5745 (ttp-110) REVERT: R 34 LYS cc_start: 0.5453 (tttt) cc_final: 0.5202 (tttp) REVERT: R 212 PHE cc_start: 0.6020 (m-80) cc_final: 0.5370 (m-10) REVERT: R 305 TYR cc_start: 0.8307 (t80) cc_final: 0.7838 (t80) REVERT: R 308 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7240 (p) REVERT: R 404 ARG cc_start: 0.6211 (tmm160) cc_final: 0.5728 (tmt-80) REVERT: R 457 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6200 (mm) REVERT: R 469 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.5325 (mm-30) outliers start: 37 outliers final: 23 residues processed: 160 average time/residue: 1.4195 time to fit residues: 240.1716 Evaluate side-chains 166 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 359 LYS Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 4 optimal weight: 0.0070 chunk 63 optimal weight: 9.9990 overall best weight: 1.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.156669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121584 restraints weight = 10099.536| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.86 r_work: 0.3316 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8910 Z= 0.166 Angle : 0.485 11.346 12090 Z= 0.261 Chirality : 0.040 0.149 1361 Planarity : 0.004 0.057 1545 Dihedral : 4.849 57.022 1234 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.34 % Allowed : 27.28 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1104 helix: 2.25 (0.25), residues: 433 sheet: -0.31 (0.33), residues: 219 loop : -0.53 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG R 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4165.22 seconds wall clock time: 74 minutes 24.42 seconds (4464.42 seconds total)