Starting phenix.real_space_refine on Tue Sep 24 17:15:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/09_2024/7vvl_32143.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/09_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_32143/09_2024/7vvl_32143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/09_2024/7vvl_32143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/09_2024/7vvl_32143.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvl_32143/09_2024/7vvl_32143.cif" } 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. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8725 Number of models: 1 Model: "" Number of chains: 7 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: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2664 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 9, 'TRANS': 336} 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 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 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: 0.97 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: 2.73 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: 0.00 - 1.81: 8531 1.81 - 3.61: 3236 3.61 - 5.42: 298 5.42 - 7.23: 18 7.23 - 9.03: 7 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 3.040 nonbonded pdb=" O GLN R 438 " pdb=" ND1 HIS R 442 " model vdw 2.262 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.265 3.120 nonbonded pdb=" OG1 THR N 28 " pdb=" ND2 ASN N 31 " model vdw 2.289 3.120 nonbonded pdb=" NH1 ARG R 282 " pdb=" OD1 ASN R 348 " model vdw 2.303 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.350 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- 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 : 0.967 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: 1.2680 time to fit residues: 290.5865 Evaluate side-chains 174 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 0.9980 chunk 83 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 P 16 ASN R 374 ASN R 402 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1803 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= 0.195 Angle : 0.539 6.768 12090 Z= 0.300 Chirality : 0.042 0.165 1361 Planarity : 0.004 0.046 1545 Dihedral : 8.876 76.549 1291 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.46 % Allowed : 21.94 % Favored : 72.61 % 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: 0.34 (0.25), residues: 1104 helix: 1.33 (0.24), residues: 444 sheet: -0.07 (0.34), residues: 212 loop : -0.69 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.002 PHE A 212 TYR 0.024 0.002 TYR R 191 ARG 0.005 0.001 ARG N 72 *********************** 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 200 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 151 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6436 (pt0) REVERT: A 27 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6463 (mm-30) REVERT: A 28 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6540 (mtpt) REVERT: A 49 ASP cc_start: 0.7260 (m-30) cc_final: 0.6655 (t0) REVERT: A 58 LYS cc_start: 0.6183 (mtpp) cc_final: 0.5920 (mmtp) REVERT: A 289 GLU cc_start: 0.7491 (pp20) cc_final: 0.7019 (tp30) REVERT: A 346 ARG cc_start: 0.7145 (mmm-85) cc_final: 0.6374 (mtm-85) REVERT: B 27 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5735 (p0) REVERT: B 32 GLN cc_start: 0.5995 (pt0) cc_final: 0.5516 (tp40) REVERT: B 66 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7261 (p0) REVERT: B 70 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8409 (pp) REVERT: B 96 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7185 (ttm-80) REVERT: B 101 MET cc_start: 0.8677 (mtp) cc_final: 0.8215 (mtp) REVERT: B 124 TYR cc_start: 0.8414 (m-80) cc_final: 0.7987 (m-80) REVERT: B 137 ARG cc_start: 0.7104 (ttm110) cc_final: 0.6840 (ttm110) REVERT: B 138 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 146 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8296 (tt) REVERT: B 156 GLN cc_start: 0.7439 (mt0) cc_final: 0.7192 (mt0) REVERT: B 176 GLN cc_start: 0.8118 (tt0) cc_final: 0.7912 (tt0) REVERT: B 220 GLN cc_start: 0.8074 (mt0) cc_final: 0.7861 (mt0) REVERT: G 44 HIS cc_start: 0.7605 (m90) cc_final: 0.7398 (m-70) REVERT: N 3 GLN cc_start: 0.6522 (tt0) cc_final: 0.6035 (tt0) REVERT: N 39 GLN cc_start: 0.8329 (tt0) cc_final: 0.7925 (tt0) REVERT: N 53 GLN cc_start: 0.7282 (mp10) cc_final: 0.6632 (mp10) REVERT: N 80 TYR cc_start: 0.7778 (m-80) cc_final: 0.6326 (m-80) REVERT: N 83 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6686 (mtt) REVERT: N 95 TYR cc_start: 0.8507 (m-80) cc_final: 0.8045 (m-80) REVERT: N 104 THR cc_start: 0.7994 (p) cc_final: 0.7593 (p) REVERT: N 105 ARG cc_start: 0.6836 (ttt180) cc_final: 0.6418 (mmm-85) REVERT: N 106 ASP cc_start: 0.8472 (p0) cc_final: 0.8152 (p0) REVERT: N 123 GLN cc_start: 0.6812 (mm-40) cc_final: 0.6499 (tp-100) REVERT: R 182 GLU cc_start: 0.7570 (tt0) cc_final: 0.7340 (tt0) REVERT: R 189 MET cc_start: 0.7252 (tpt) cc_final: 0.7014 (tpp) REVERT: R 218 THR cc_start: 0.8121 (t) cc_final: 0.7833 (m) REVERT: R 305 TYR cc_start: 0.8310 (t80) cc_final: 0.7616 (t80) REVERT: R 318 LYS cc_start: 0.5845 (mppt) cc_final: 0.5622 (mmtt) REVERT: R 346 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7171 (mm) REVERT: R 390 ARG cc_start: 0.7002 (ttp80) cc_final: 0.6772 (ttp-110) REVERT: R 404 ARG cc_start: 0.5906 (tmm160) cc_final: 0.5255 (tmt-80) REVERT: R 441 MET cc_start: 0.8240 (mmt) cc_final: 0.8022 (mmt) outliers start: 49 outliers final: 22 residues processed: 184 average time/residue: 1.2604 time to fit residues: 246.3754 Evaluate side-chains 167 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 304 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 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 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 78 THR Chi-restraints excluded: chain N residue 83 MET 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 N residue 125 THR 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 346 LEU 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: 6.9990 chunk 31 optimal weight: 10.0000 chunk 83 optimal weight: 0.0070 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 175 GLN B 237 ASN B 340 ASN N 31 ASN P 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8910 Z= 0.192 Angle : 0.498 6.233 12090 Z= 0.276 Chirality : 0.041 0.160 1361 Planarity : 0.004 0.052 1545 Dihedral : 7.651 75.510 1258 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.79 % Allowed : 22.83 % Favored : 71.38 % 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: 0.61 (0.25), residues: 1104 helix: 1.76 (0.25), residues: 444 sheet: -0.11 (0.33), residues: 213 loop : -0.68 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.016 0.001 PHE A 212 TYR 0.024 0.001 TYR R 191 ARG 0.004 0.000 ARG N 72 *********************** 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 197 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 145 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6600 (pt0) REVERT: A 27 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6529 (mm-30) REVERT: A 28 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6572 (mtpt) REVERT: A 49 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6736 (t0) REVERT: A 289 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: B 27 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5772 (p0) REVERT: B 32 GLN cc_start: 0.5971 (pt0) cc_final: 0.5658 (tp40) REVERT: B 38 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7140 (p0) REVERT: B 66 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7441 (p0) REVERT: B 96 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7163 (ttm-80) REVERT: B 101 MET cc_start: 0.8664 (mtp) cc_final: 0.8230 (mtp) REVERT: B 130 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.5267 (tt0) REVERT: B 137 ARG cc_start: 0.7109 (ttm110) cc_final: 0.6841 (ttm110) REVERT: B 138 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7637 (mt-10) REVERT: B 146 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8406 (tt) REVERT: B 156 GLN cc_start: 0.7461 (mt0) cc_final: 0.7193 (mt0) REVERT: G 44 HIS cc_start: 0.7644 (m90) cc_final: 0.7428 (m-70) REVERT: N 3 GLN cc_start: 0.6456 (tt0) cc_final: 0.5954 (tt0) REVERT: N 39 GLN cc_start: 0.8354 (tt0) cc_final: 0.8008 (tt0) REVERT: N 53 GLN cc_start: 0.7227 (mp10) cc_final: 0.6590 (mp10) REVERT: N 80 TYR cc_start: 0.7690 (m-80) cc_final: 0.6216 (m-80) REVERT: N 86 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7008 (mp) REVERT: N 105 ARG cc_start: 0.6833 (ttt180) cc_final: 0.6234 (ttp-170) REVERT: N 106 ASP cc_start: 0.8464 (p0) cc_final: 0.8218 (p0) REVERT: N 123 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6784 (tp-100) REVERT: R 45 GLN cc_start: 0.5835 (OUTLIER) cc_final: 0.4751 (tt0) REVERT: R 218 THR cc_start: 0.8115 (t) cc_final: 0.7825 (m) REVERT: R 240 LYS cc_start: 0.6865 (ttpt) cc_final: 0.6498 (ttpp) REVERT: R 305 TYR cc_start: 0.8378 (t80) cc_final: 0.7667 (t80) REVERT: R 308 SER cc_start: 0.7683 (OUTLIER) cc_final: 0.7199 (p) REVERT: R 318 LYS cc_start: 0.5878 (mppt) cc_final: 0.5666 (mmtt) REVERT: R 390 ARG cc_start: 0.7051 (ttp80) cc_final: 0.6842 (ttp-110) REVERT: R 404 ARG cc_start: 0.6064 (tmm160) cc_final: 0.5485 (tmt-80) outliers start: 52 outliers final: 25 residues processed: 178 average time/residue: 1.3188 time to fit residues: 248.9454 Evaluate side-chains 174 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 289 GLU 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 130 GLU Chi-restraints excluded: chain B residue 146 LEU 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 71 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 N residue 125 THR Chi-restraints excluded: chain P residue 13 LYS 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 359 LYS 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: 5.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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** P 16 ASN R 223 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8910 Z= 0.291 Angle : 0.562 7.852 12090 Z= 0.306 Chirality : 0.044 0.175 1361 Planarity : 0.004 0.056 1545 Dihedral : 7.542 78.271 1253 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 7.02 % Allowed : 23.50 % Favored : 69.49 % 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: 0.43 (0.25), residues: 1104 helix: 1.66 (0.25), residues: 439 sheet: -0.31 (0.33), residues: 220 loop : -0.74 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS R 420 PHE 0.017 0.002 PHE A 212 TYR 0.024 0.002 TYR R 191 ARG 0.004 0.001 ARG A 228 *********************** 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 200 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 137 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: A 27 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6567 (mm-30) REVERT: A 28 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6602 (mtpt) REVERT: A 289 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7003 (tp30) REVERT: B 27 ASP cc_start: 0.6171 (OUTLIER) cc_final: 0.5694 (p0) REVERT: B 32 GLN cc_start: 0.5961 (pt0) cc_final: 0.5652 (tp40) REVERT: B 96 ARG cc_start: 0.7464 (mtm110) cc_final: 0.7129 (ttm-80) REVERT: B 101 MET cc_start: 0.8712 (mtp) cc_final: 0.8354 (mtp) REVERT: B 124 TYR cc_start: 0.8387 (m-80) cc_final: 0.7851 (m-80) REVERT: B 130 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.5031 (tt0) REVERT: B 137 ARG cc_start: 0.7059 (ttm110) cc_final: 0.6779 (ttm110) REVERT: B 138 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7662 (mt-10) REVERT: B 156 GLN cc_start: 0.7526 (mt0) cc_final: 0.7278 (mt0) REVERT: N 3 GLN cc_start: 0.6471 (tt0) cc_final: 0.5969 (tt0) REVERT: N 39 GLN cc_start: 0.8383 (tt0) cc_final: 0.7995 (tt0) REVERT: N 53 GLN cc_start: 0.7289 (mp10) cc_final: 0.6633 (mp10) REVERT: N 80 TYR cc_start: 0.7800 (m-80) cc_final: 0.6496 (m-80) REVERT: N 86 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7104 (mp) REVERT: R 34 LYS cc_start: 0.5625 (ttpp) cc_final: 0.5135 (tttp) REVERT: R 218 THR cc_start: 0.8062 (t) cc_final: 0.7844 (m) REVERT: R 305 TYR cc_start: 0.8403 (t80) cc_final: 0.8041 (t80) REVERT: R 318 LYS cc_start: 0.5858 (mppt) cc_final: 0.5615 (mmpt) REVERT: R 469 GLU cc_start: 0.5555 (mm-30) cc_final: 0.5343 (mm-30) outliers start: 63 outliers final: 36 residues processed: 180 average time/residue: 1.3074 time to fit residues: 249.8780 Evaluate side-chains 177 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 135 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 29 GLN 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 304 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 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 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 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 N residue 125 THR Chi-restraints excluded: chain P residue 13 LYS 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 363 ILE Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 408 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 0.3980 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 0.2980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** G 44 HIS P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8910 Z= 0.261 Angle : 0.542 7.702 12090 Z= 0.295 Chirality : 0.043 0.168 1361 Planarity : 0.004 0.057 1545 Dihedral : 7.218 80.024 1251 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.68 % Allowed : 23.94 % Favored : 69.38 % 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: 0.38 (0.25), residues: 1104 helix: 1.64 (0.25), residues: 439 sheet: -0.39 (0.33), residues: 220 loop : -0.76 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.018 0.002 PHE R 230 TYR 0.023 0.002 TYR R 191 ARG 0.004 0.001 ARG A 228 *********************** 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 200 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 140 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6618 (tm-30) REVERT: A 27 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6566 (mm-30) REVERT: A 28 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6669 (mtpt) REVERT: A 289 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: B 27 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.5736 (p0) REVERT: B 32 GLN cc_start: 0.5887 (pt0) cc_final: 0.5640 (tp40) REVERT: B 96 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7135 (ttm-80) REVERT: B 101 MET cc_start: 0.8693 (mtp) cc_final: 0.8261 (mtp) REVERT: B 130 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5244 (tt0) REVERT: B 137 ARG cc_start: 0.7107 (ttm110) cc_final: 0.6760 (tpp80) REVERT: B 138 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7623 (mt-10) REVERT: B 156 GLN cc_start: 0.7453 (mt0) cc_final: 0.7200 (mt0) REVERT: B 201 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8732 (p) REVERT: N 3 GLN cc_start: 0.6491 (tt0) cc_final: 0.5972 (tt0) REVERT: N 39 GLN cc_start: 0.8399 (tt0) cc_final: 0.8007 (tt0) REVERT: N 53 GLN cc_start: 0.7273 (mp10) cc_final: 0.6604 (mp10) REVERT: N 80 TYR cc_start: 0.7768 (m-80) cc_final: 0.6390 (m-80) REVERT: N 86 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7169 (mp) REVERT: N 105 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6382 (mmm-85) REVERT: N 125 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7436 (p) REVERT: R 34 LYS cc_start: 0.5568 (ttpp) cc_final: 0.5065 (tttp) REVERT: R 218 THR cc_start: 0.8104 (t) cc_final: 0.7902 (m) REVERT: R 305 TYR cc_start: 0.8418 (t80) cc_final: 0.8017 (t80) REVERT: R 317 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6076 (mp0) REVERT: R 318 LYS cc_start: 0.6003 (mppt) cc_final: 0.5690 (mmtt) REVERT: R 390 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6889 (ttp-110) REVERT: R 425 MET cc_start: 0.8455 (pp-130) cc_final: 0.8173 (ptm) REVERT: R 469 GLU cc_start: 0.5562 (mm-30) cc_final: 0.5328 (mm-30) outliers start: 60 outliers final: 33 residues processed: 183 average time/residue: 1.3414 time to fit residues: 260.1795 Evaluate side-chains 179 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 29 GLN 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 304 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 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 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 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 71 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 105 ARG 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 25 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 G 44 HIS P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8910 Z= 0.188 Angle : 0.501 8.141 12090 Z= 0.274 Chirality : 0.041 0.158 1361 Planarity : 0.004 0.056 1545 Dihedral : 6.778 78.984 1249 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.12 % Allowed : 24.83 % 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: 0.55 (0.26), residues: 1104 helix: 1.86 (0.25), residues: 439 sheet: -0.38 (0.33), residues: 220 loop : -0.73 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.003 0.000 ARG R 179 *********************** 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 191 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 136 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: A 27 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6518 (mm-30) REVERT: A 28 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6640 (mtpt) REVERT: A 49 ASP cc_start: 0.7393 (m-30) cc_final: 0.6594 (t0) REVERT: A 289 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6907 (tp30) REVERT: B 27 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5632 (p0) REVERT: B 32 GLN cc_start: 0.5964 (pt0) cc_final: 0.5730 (tp40) REVERT: B 101 MET cc_start: 0.8742 (mtp) cc_final: 0.8362 (mtp) REVERT: B 124 TYR cc_start: 0.8405 (m-80) cc_final: 0.7807 (m-80) REVERT: B 130 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5213 (tt0) REVERT: B 137 ARG cc_start: 0.7119 (ttm110) cc_final: 0.6728 (ttm110) REVERT: B 138 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7723 (mt-10) REVERT: B 156 GLN cc_start: 0.7420 (mt0) cc_final: 0.7162 (mt0) REVERT: B 201 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8749 (p) REVERT: G 62 ARG cc_start: 0.4311 (OUTLIER) cc_final: 0.3723 (ppt170) REVERT: N 3 GLN cc_start: 0.6500 (tt0) cc_final: 0.5992 (tt0) REVERT: N 39 GLN cc_start: 0.8436 (tt0) cc_final: 0.8036 (tt0) REVERT: N 53 GLN cc_start: 0.7245 (mp10) cc_final: 0.6582 (mp10) REVERT: N 80 TYR cc_start: 0.7582 (m-80) cc_final: 0.6125 (m-80) REVERT: N 105 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6476 (mmm-85) REVERT: R 34 LYS cc_start: 0.5584 (ttpp) cc_final: 0.5111 (tttp) REVERT: R 305 TYR cc_start: 0.8373 (t80) cc_final: 0.7843 (t80) REVERT: R 308 SER cc_start: 0.7717 (OUTLIER) cc_final: 0.7231 (p) REVERT: R 317 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.6018 (mp0) REVERT: R 318 LYS cc_start: 0.6011 (mppt) cc_final: 0.5683 (mmtt) REVERT: R 390 ARG cc_start: 0.7076 (ttp80) cc_final: 0.6871 (ttp-110) REVERT: R 404 ARG cc_start: 0.5903 (tmm160) cc_final: 0.5398 (tmt-80) REVERT: R 425 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (ptm) REVERT: R 469 GLU cc_start: 0.5549 (mm-30) cc_final: 0.5249 (mm-30) outliers start: 55 outliers final: 30 residues processed: 176 average time/residue: 1.2425 time to fit residues: 232.8149 Evaluate side-chains 174 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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 97 SER Chi-restraints excluded: chain B residue 98 SER 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 207 SER 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 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR 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 114 THR Chi-restraints excluded: chain P residue 13 LYS 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 0.0170 chunk 77 optimal weight: 40.0000 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 75 GLN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN G 44 HIS P 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8910 Z= 0.154 Angle : 0.480 8.592 12090 Z= 0.263 Chirality : 0.040 0.153 1361 Planarity : 0.004 0.055 1545 Dihedral : 5.877 58.689 1245 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.12 % Allowed : 25.95 % 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: 0.71 (0.26), residues: 1104 helix: 2.06 (0.26), residues: 439 sheet: -0.25 (0.33), residues: 215 loop : -0.73 (0.29), residues: 450 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 0.017 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.003 0.000 ARG B 197 *********************** 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 180 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 134 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6519 (mm-30) REVERT: A 28 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6684 (mtpt) REVERT: A 49 ASP cc_start: 0.7362 (m-30) cc_final: 0.6592 (t0) REVERT: A 273 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7507 (ptm160) REVERT: A 285 ASP cc_start: 0.7565 (t0) cc_final: 0.7244 (p0) REVERT: A 289 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: B 27 ASP cc_start: 0.6169 (OUTLIER) cc_final: 0.5678 (p0) REVERT: B 70 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8141 (pp) REVERT: B 101 MET cc_start: 0.8764 (mtp) cc_final: 0.8305 (mtp) REVERT: B 124 TYR cc_start: 0.8338 (m-80) cc_final: 0.7775 (m-80) REVERT: B 130 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.5235 (tt0) REVERT: B 137 ARG cc_start: 0.7100 (ttm110) cc_final: 0.6721 (ttm110) REVERT: B 138 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 156 GLN cc_start: 0.7402 (mt0) cc_final: 0.7146 (mt0) REVERT: B 201 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8801 (p) REVERT: G 62 ARG cc_start: 0.4518 (OUTLIER) cc_final: 0.4077 (ppt170) REVERT: N 3 GLN cc_start: 0.6523 (tt0) cc_final: 0.6025 (tt0) REVERT: N 39 GLN cc_start: 0.8430 (tt0) cc_final: 0.8085 (tt0) REVERT: N 46 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7730 (mt-10) REVERT: N 53 GLN cc_start: 0.7316 (mp10) cc_final: 0.6612 (mp10) REVERT: N 80 TYR cc_start: 0.7544 (m-80) cc_final: 0.5977 (m-80) REVERT: N 105 ARG cc_start: 0.6895 (ttt180) cc_final: 0.6300 (ttp-170) REVERT: R 305 TYR cc_start: 0.8346 (t80) cc_final: 0.7910 (t80) REVERT: R 308 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7245 (p) REVERT: R 390 ARG cc_start: 0.7060 (ttp80) cc_final: 0.6852 (ttp-110) REVERT: R 404 ARG cc_start: 0.5989 (tmm160) cc_final: 0.5503 (tmt-80) REVERT: R 425 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8167 (ptm) outliers start: 46 outliers final: 25 residues processed: 166 average time/residue: 1.2994 time to fit residues: 229.1293 Evaluate side-chains 167 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 SER 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 207 SER 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 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 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 217 CYS 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 425 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 0.0170 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.1422 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8910 Z= 0.162 Angle : 0.488 9.316 12090 Z= 0.265 Chirality : 0.040 0.154 1361 Planarity : 0.004 0.056 1545 Dihedral : 5.288 58.388 1240 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.68 % Allowed : 27.51 % Favored : 67.82 % 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: 0.77 (0.26), residues: 1104 helix: 2.14 (0.25), residues: 439 sheet: -0.29 (0.33), residues: 217 loop : -0.70 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 0.003 0.000 ARG B 197 *********************** 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 176 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6560 (mm-30) REVERT: A 28 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6646 (mtpt) REVERT: A 49 ASP cc_start: 0.7362 (m-30) cc_final: 0.6578 (t0) REVERT: A 273 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7585 (ptm160) REVERT: A 285 ASP cc_start: 0.7528 (t0) cc_final: 0.7237 (p0) REVERT: A 289 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: B 27 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5671 (p0) REVERT: B 101 MET cc_start: 0.8796 (mtp) cc_final: 0.8433 (mtp) REVERT: B 124 TYR cc_start: 0.8330 (m-80) cc_final: 0.7819 (m-80) REVERT: B 130 GLU cc_start: 0.5786 (OUTLIER) cc_final: 0.5230 (tt0) REVERT: B 137 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6838 (ttm110) REVERT: B 138 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7708 (mt-10) REVERT: B 156 GLN cc_start: 0.7421 (mt0) cc_final: 0.7165 (mt0) REVERT: B 201 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8839 (p) REVERT: N 3 GLN cc_start: 0.6516 (tt0) cc_final: 0.6011 (tt0) REVERT: N 39 GLN cc_start: 0.8436 (tt0) cc_final: 0.8127 (tt0) REVERT: N 46 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7728 (mt-10) REVERT: N 53 GLN cc_start: 0.7288 (mp10) cc_final: 0.6601 (mp10) REVERT: N 80 TYR cc_start: 0.7481 (m-80) cc_final: 0.5898 (m-80) REVERT: N 105 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6306 (ttp-170) REVERT: R 34 LYS cc_start: 0.5549 (ttpp) cc_final: 0.5058 (tttp) REVERT: R 305 TYR cc_start: 0.8352 (t80) cc_final: 0.7810 (t80) REVERT: R 308 SER cc_start: 0.7690 (OUTLIER) cc_final: 0.7265 (p) REVERT: R 317 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: R 390 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6979 (ttp-110) REVERT: R 404 ARG cc_start: 0.6011 (tmm160) cc_final: 0.5531 (tmt-80) outliers start: 42 outliers final: 27 residues processed: 163 average time/residue: 1.3237 time to fit residues: 228.5680 Evaluate side-chains 164 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 97 SER Chi-restraints excluded: chain B residue 98 SER 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 207 SER 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 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 105 ARG 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 R residue 217 CYS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3049 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= 0.148 Angle : 0.487 10.918 12090 Z= 0.263 Chirality : 0.040 0.150 1361 Planarity : 0.004 0.055 1545 Dihedral : 4.865 57.282 1234 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.01 % Allowed : 27.62 % 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: 0.86 (0.26), residues: 1104 helix: 2.24 (0.25), residues: 439 sheet: -0.23 (0.34), residues: 216 loop : -0.68 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.003 0.000 ARG B 197 *********************** 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 170 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6500 (mm-30) REVERT: A 28 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6470 (mtpt) REVERT: A 49 ASP cc_start: 0.7357 (m-30) cc_final: 0.6626 (t0) REVERT: A 273 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7523 (ptm160) REVERT: A 285 ASP cc_start: 0.7466 (t0) cc_final: 0.7201 (p0) REVERT: A 289 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: B 27 ASP cc_start: 0.6086 (OUTLIER) cc_final: 0.5587 (p0) REVERT: B 101 MET cc_start: 0.8755 (mtp) cc_final: 0.8400 (mtp) REVERT: B 130 GLU cc_start: 0.5776 (OUTLIER) cc_final: 0.5227 (tt0) REVERT: B 137 ARG cc_start: 0.7132 (ttm110) cc_final: 0.6851 (ttm110) REVERT: B 138 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7702 (mt-10) REVERT: B 156 GLN cc_start: 0.7437 (mt0) cc_final: 0.7179 (mt0) REVERT: N 3 GLN cc_start: 0.6514 (tt0) cc_final: 0.6005 (tt0) REVERT: N 39 GLN cc_start: 0.8405 (tt0) cc_final: 0.8116 (tt0) REVERT: N 46 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7644 (mt-10) REVERT: N 53 GLN cc_start: 0.7333 (mp10) cc_final: 0.6763 (mp10) REVERT: N 80 TYR cc_start: 0.7495 (m-80) cc_final: 0.5885 (m-80) REVERT: N 105 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6256 (ttp-170) REVERT: R 34 LYS cc_start: 0.5515 (ttpp) cc_final: 0.5043 (tttp) REVERT: R 278 TYR cc_start: 0.5593 (OUTLIER) cc_final: 0.3875 (t80) REVERT: R 308 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.7143 (p) REVERT: R 404 ARG cc_start: 0.5946 (tmm160) cc_final: 0.5475 (tmt-80) outliers start: 36 outliers final: 23 residues processed: 162 average time/residue: 1.2881 time to fit residues: 221.3917 Evaluate side-chains 162 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 273 ARG Chi-restraints excluded: chain A residue 289 GLU 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 207 SER 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 N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 71 SER 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 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 197 VAL 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 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 408 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8910 Z= 0.177 Angle : 0.505 11.351 12090 Z= 0.271 Chirality : 0.041 0.156 1361 Planarity : 0.004 0.057 1545 Dihedral : 4.936 57.307 1234 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.68 % Allowed : 26.84 % 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: 0.84 (0.26), residues: 1104 helix: 2.21 (0.25), residues: 439 sheet: -0.20 (0.34), residues: 215 loop : -0.72 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.003 0.000 ARG B 197 ********************** 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 175 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6557 (mm-30) REVERT: A 28 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6576 (mtpt) REVERT: A 49 ASP cc_start: 0.7245 (m-30) cc_final: 0.6523 (t0) REVERT: A 273 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7523 (ptm160) REVERT: A 285 ASP cc_start: 0.7476 (t0) cc_final: 0.7198 (p0) REVERT: A 289 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6956 (tp30) REVERT: B 101 MET cc_start: 0.8779 (mtp) cc_final: 0.8410 (mtp) REVERT: B 130 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5225 (tt0) REVERT: B 137 ARG cc_start: 0.7124 (ttm110) cc_final: 0.6825 (ttm110) REVERT: B 138 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7701 (mt-10) REVERT: B 156 GLN cc_start: 0.7482 (mt0) cc_final: 0.7226 (mt0) REVERT: N 3 GLN cc_start: 0.6442 (tt0) cc_final: 0.5934 (tt0) REVERT: N 39 GLN cc_start: 0.8452 (tt0) cc_final: 0.8142 (tt0) REVERT: N 46 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7748 (mt-10) REVERT: N 53 GLN cc_start: 0.7294 (mp10) cc_final: 0.6607 (mp10) REVERT: N 80 TYR cc_start: 0.7483 (m-80) cc_final: 0.5953 (m-80) REVERT: N 105 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6287 (ttp-170) REVERT: R 34 LYS cc_start: 0.5498 (ttpp) cc_final: 0.5025 (tttp) REVERT: R 278 TYR cc_start: 0.5595 (OUTLIER) cc_final: 0.3722 (t80) REVERT: R 305 TYR cc_start: 0.8326 (t80) cc_final: 0.7821 (t80) REVERT: R 308 SER cc_start: 0.7687 (OUTLIER) cc_final: 0.7275 (p) REVERT: R 404 ARG cc_start: 0.5915 (tmm160) cc_final: 0.5443 (tmt-80) outliers start: 42 outliers final: 26 residues processed: 165 average time/residue: 1.3211 time to fit residues: 231.1559 Evaluate side-chains 167 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER 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 207 SER 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 70 ILE Chi-restraints excluded: chain N residue 71 SER 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 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 197 VAL 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 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 408 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.0070 chunk 36 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.158763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123585 restraints weight = 10090.434| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.89 r_work: 0.3344 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8910 Z= 0.137 Angle : 0.484 11.334 12090 Z= 0.260 Chirality : 0.040 0.149 1361 Planarity : 0.004 0.055 1545 Dihedral : 4.757 56.795 1234 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.56 % Allowed : 27.84 % Favored : 68.60 % 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: 0.93 (0.26), residues: 1104 helix: 2.34 (0.25), residues: 439 sheet: -0.22 (0.34), residues: 216 loop : -0.69 (0.29), residues: 449 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 0.024 0.001 TYR R 191 ARG 0.003 0.000 ARG R 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4124.82 seconds wall clock time: 72 minutes 24.30 seconds (4344.30 seconds total)