Starting phenix.real_space_refine on Sat Jan 20 00:33:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/01_2024/8uoy_42441.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/01_2024/8uoy_42441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/01_2024/8uoy_42441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/01_2024/8uoy_42441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/01_2024/8uoy_42441.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/01_2024/8uoy_42441.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 4182 2.51 5 N 1122 2.21 5 O 1318 1.98 5 H 6544 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 22": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 320": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13188 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 6.01, per 1000 atoms: 0.46 Number of scatterers: 13188 At special positions: 0 Unit cell: (119.658, 76.538, 86.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 1318 8.00 N 1122 7.00 C 4182 6.00 H 6544 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 43.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.562A pdb=" N ALA B 78 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.944A pdb=" N ALA B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 127 removed outlier: 3.516A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 152 through 156 removed outlier: 4.281A pdb=" N HIS B 155 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER B 156 " --> pdb=" O GLY B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 156' Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.660A pdb=" N HIS B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 229 removed outlier: 4.156A pdb=" N ILE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 259 through 262 Processing helix chain 'B' and resid 273 through 280 removed outlier: 3.866A pdb=" N ASP B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 310 removed outlier: 4.261A pdb=" N GLU B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 346 through 349 removed outlier: 3.785A pdb=" N GLY B 349 " --> pdb=" O ASN B 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 380 through 390 removed outlier: 4.170A pdb=" N ALA B 386 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 407 through 416 removed outlier: 4.413A pdb=" N ARG B 413 " --> pdb=" O ASN B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 64 through 79 removed outlier: 5.887A pdb=" N ASN C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 99 removed outlier: 3.581A pdb=" N ILE C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.521A pdb=" N SER C 156 " --> pdb=" O GLY C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.953A pdb=" N ALA C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 229 removed outlier: 3.936A pdb=" N VAL C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 271 through 280 removed outlier: 3.507A pdb=" N GLU C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 299 through 311 removed outlier: 4.415A pdb=" N THR C 307 " --> pdb=" O TRP C 303 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.685A pdb=" N LYS C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'C' and resid 350 through 365 removed outlier: 3.705A pdb=" N ALA C 364 " --> pdb=" O MET C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.690A pdb=" N ASP C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 409 removed outlier: 4.674A pdb=" N LYS C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 419 removed outlier: 5.245A pdb=" N GLU C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 422 No H-bonds generated for 'chain 'C' and resid 420 through 422' Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 14 removed outlier: 4.036A pdb=" N ASP B 6 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 12 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 144 through 145 removed outlier: 6.252A pdb=" N THR B 144 " --> pdb=" O ILE B 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 169 removed outlier: 3.836A pdb=" N GLU B 164 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ILE B 288 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 240 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE B 289 " --> pdb=" O GLN B 315 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 317 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 291 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU B 316 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 342 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 318 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS B 344 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 341 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N SER B 371 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 343 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 10 removed outlier: 4.227A pdb=" N TYR C 8 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 144 through 151 removed outlier: 5.462A pdb=" N ASN C 148 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE C 167 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 150 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 240 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLU C 292 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE C 242 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA C 368 " --> pdb=" O GLN C 393 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS C 395 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 370 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 144 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 250 through 251 228 hydrogen bonds defined for protein. 648 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: 4.76 Time building geometry restraints manager: 11.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.08: 1954 1.08 - 1.27: 5778 1.27 - 1.46: 1743 1.46 - 1.65: 3777 1.65 - 1.83: 42 Bond restraints: 13294 Sorted by residual: bond pdb=" CG ASP B 301 " pdb=" OD1 ASP B 301 " ideal model delta sigma weight residual 1.249 1.080 0.169 1.90e-02 2.77e+03 7.93e+01 bond pdb=" CB ASP B 301 " pdb=" CG ASP B 301 " ideal model delta sigma weight residual 1.516 1.322 0.194 2.50e-02 1.60e+03 6.01e+01 bond pdb=" CE1 TYR C 59 " pdb=" HE1 TYR C 59 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LEU C 351 " pdb=" H LEU C 351 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N LEU B 51 " pdb=" H LEU B 51 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 ... (remaining 13289 not shown) Histogram of bond angle deviations from ideal: 97.49 - 105.09: 262 105.09 - 112.70: 14442 112.70 - 120.30: 6228 120.30 - 127.91: 3010 127.91 - 135.51: 80 Bond angle restraints: 24022 Sorted by residual: angle pdb=" CA PHE C 249 " pdb=" CB PHE C 249 " pdb=" CG PHE C 249 " ideal model delta sigma weight residual 113.80 122.09 -8.29 1.00e+00 1.00e+00 6.87e+01 angle pdb=" CA ASN C 236 " pdb=" CB ASN C 236 " pdb=" CG ASN C 236 " ideal model delta sigma weight residual 112.60 120.58 -7.98 1.00e+00 1.00e+00 6.36e+01 angle pdb=" C LEU B 62 " pdb=" N GLY B 63 " pdb=" CA GLY B 63 " ideal model delta sigma weight residual 120.31 128.40 -8.09 1.02e+00 9.61e-01 6.30e+01 angle pdb=" CA ASN C 284 " pdb=" CB ASN C 284 " pdb=" CG ASN C 284 " ideal model delta sigma weight residual 112.60 120.24 -7.64 1.00e+00 1.00e+00 5.83e+01 angle pdb=" CA ASP B 301 " pdb=" CB ASP B 301 " pdb=" CG ASP B 301 " ideal model delta sigma weight residual 112.60 120.21 -7.61 1.00e+00 1.00e+00 5.79e+01 ... (remaining 24017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 5305 16.79 - 33.59: 519 33.59 - 50.38: 122 50.38 - 67.17: 70 67.17 - 83.97: 16 Dihedral angle restraints: 6032 sinusoidal: 3210 harmonic: 2822 Sorted by residual: dihedral pdb=" C ILE B 222 " pdb=" N ILE B 222 " pdb=" CA ILE B 222 " pdb=" CB ILE B 222 " ideal model delta harmonic sigma weight residual -122.00 -140.12 18.12 0 2.50e+00 1.60e-01 5.25e+01 dihedral pdb=" CA MET B 239 " pdb=" C MET B 239 " pdb=" N ILE B 240 " pdb=" CA ILE B 240 " ideal model delta harmonic sigma weight residual 180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA HIS C 372 " pdb=" C HIS C 372 " pdb=" N ARG C 373 " pdb=" CA ARG C 373 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 6029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 703 0.106 - 0.213: 258 0.213 - 0.319: 54 0.319 - 0.425: 7 0.425 - 0.532: 4 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CA THR B 64 " pdb=" N THR B 64 " pdb=" C THR B 64 " pdb=" CB THR B 64 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CA ILE B 222 " pdb=" N ILE B 222 " pdb=" C ILE B 222 " pdb=" CB ILE B 222 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" CA LYS C 434 " pdb=" N LYS C 434 " pdb=" C LYS C 434 " pdb=" CB LYS C 434 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 1023 not shown) Planarity restraints: 2046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 181 " -0.316 2.00e-02 2.50e+03 1.10e-01 4.81e+02 pdb=" CG TRP C 181 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP C 181 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TRP C 181 " 0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP C 181 " 0.116 2.00e-02 2.50e+03 pdb=" CE2 TRP C 181 " 0.043 2.00e-02 2.50e+03 pdb=" CE3 TRP C 181 " 0.092 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 181 " -0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 181 " 0.042 2.00e-02 2.50e+03 pdb=" CH2 TRP C 181 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 TRP C 181 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP C 181 " 0.075 2.00e-02 2.50e+03 pdb=" HE3 TRP C 181 " 0.126 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 181 " -0.107 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 181 " 0.044 2.00e-02 2.50e+03 pdb=" HH2 TRP C 181 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 82 " -0.267 2.00e-02 2.50e+03 1.09e-01 3.55e+02 pdb=" CG TYR B 82 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 82 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR B 82 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR B 82 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR B 82 " 0.049 2.00e-02 2.50e+03 pdb=" CZ TYR B 82 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR B 82 " -0.201 2.00e-02 2.50e+03 pdb=" HD1 TYR B 82 " 0.066 2.00e-02 2.50e+03 pdb=" HD2 TYR B 82 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 TYR B 82 " 0.031 2.00e-02 2.50e+03 pdb=" HE2 TYR B 82 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 34 " -0.679 9.50e-02 1.11e+02 2.47e-01 2.71e+02 pdb=" NE ARG B 34 " -0.084 2.00e-02 2.50e+03 pdb=" CZ ARG B 34 " -0.057 2.00e-02 2.50e+03 pdb=" NH1 ARG B 34 " -0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG B 34 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG B 34 " 0.208 2.00e-02 2.50e+03 pdb="HH12 ARG B 34 " -0.072 2.00e-02 2.50e+03 pdb="HH21 ARG B 34 " 0.154 2.00e-02 2.50e+03 pdb="HH22 ARG B 34 " -0.034 2.00e-02 2.50e+03 ... (remaining 2043 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 925 2.18 - 2.79: 23119 2.79 - 3.39: 37363 3.39 - 4.00: 47978 4.00 - 4.60: 71199 Nonbonded interactions: 180584 Sorted by model distance: nonbonded pdb=" HG SER C 246 " pdb=" O ASP C 293 " model vdw 1.575 1.850 nonbonded pdb=" HG SER B 247 " pdb=" OD1 ASP B 296 " model vdw 1.590 1.850 nonbonded pdb=" OD1 ASP C 98 " pdb=" HG1 THR C 100 " model vdw 1.593 1.850 nonbonded pdb=" HH TYR B 257 " pdb=" OD2 ASP B 299 " model vdw 1.601 1.850 nonbonded pdb=" HG1 THR C 271 " pdb=" OE1 GLU C 274 " model vdw 1.603 1.850 ... (remaining 180579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 0.520 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: 0.200 Extract box with map and model: 2.840 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 45.050 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2472 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 : 0.016 0.194 6750 Z= 1.011 Angle : 2.246 11.081 9128 Z= 1.461 Chirality : 0.113 0.532 1026 Planarity : 0.019 0.226 1198 Dihedral : 17.124 83.965 2470 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 2.65 % Allowed : 12.10 % Favored : 85.25 % Rotamer: Outliers : 6.89 % Allowed : 9.24 % Favored : 83.87 % Cbeta Deviations : 1.28 % 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: -3.89 (0.24), residues: 868 helix: -3.32 (0.20), residues: 303 sheet: -1.58 (0.76), residues: 45 loop : -2.27 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.209 0.039 TRP C 181 HIS 0.013 0.004 HIS C 155 PHE 0.128 0.019 PHE C 249 TYR 0.229 0.028 TYR B 82 ARG 0.008 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 76 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 ASP cc_start: 0.6247 (p0) cc_final: 0.4792 (m-30) REVERT: B 36 MET cc_start: -0.0763 (OUTLIER) cc_final: -0.2783 (pmt) REVERT: B 65 GLN cc_start: 0.3000 (tp40) cc_final: 0.1920 (tp40) REVERT: B 124 ASP cc_start: 0.2300 (OUTLIER) cc_final: 0.2040 (m-30) REVERT: B 213 GLU cc_start: 0.3711 (OUTLIER) cc_final: 0.2470 (tp30) REVERT: B 274 GLU cc_start: 0.2338 (OUTLIER) cc_final: 0.1553 (mt-10) REVERT: B 282 LEU cc_start: 0.1614 (OUTLIER) cc_final: 0.0884 (tt) REVERT: B 284 ASN cc_start: 0.3150 (OUTLIER) cc_final: 0.0099 (m-40) REVERT: B 301 ASP cc_start: 0.2824 (OUTLIER) cc_final: 0.2159 (t0) REVERT: B 309 ARG cc_start: 0.4183 (OUTLIER) cc_final: 0.2288 (tpt170) REVERT: C 1 MET cc_start: 0.2811 (mmt) cc_final: 0.2411 (mmt) REVERT: C 77 GLU cc_start: 0.0585 (OUTLIER) cc_final: -0.0524 (pp20) REVERT: C 85 ARG cc_start: 0.3713 (mtm180) cc_final: 0.0640 (ttp80) REVERT: C 181 TRP cc_start: 0.2747 (OUTLIER) cc_final: 0.2026 (m-10) REVERT: C 261 LYS cc_start: 0.3104 (tptt) cc_final: 0.2755 (tptp) REVERT: C 362 LYS cc_start: 0.2445 (OUTLIER) cc_final: 0.0412 (tmmt) outliers start: 47 outliers final: 25 residues processed: 119 average time/residue: 0.4309 time to fit residues: 67.4118 Evaluate side-chains 97 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 61 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2377 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 6750 Z= 0.299 Angle : 0.877 10.692 9128 Z= 0.478 Chirality : 0.047 0.169 1026 Planarity : 0.006 0.068 1198 Dihedral : 12.673 65.830 1029 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.60 % Favored : 88.94 % Rotamer: Outliers : 6.45 % Allowed : 13.05 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.83 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.25), residues: 868 helix: -2.28 (0.26), residues: 293 sheet: -2.91 (0.45), residues: 102 loop : -2.11 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 181 HIS 0.005 0.002 HIS B 0 PHE 0.027 0.003 PHE B 249 TYR 0.024 0.002 TYR B 408 ARG 0.005 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 58 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: -0.0857 (OUTLIER) cc_final: -0.3070 (pmt) REVERT: B 124 ASP cc_start: 0.1072 (OUTLIER) cc_final: 0.0725 (m-30) REVERT: B 126 LEU cc_start: 0.0056 (OUTLIER) cc_final: -0.1626 (mt) REVERT: B 132 THR cc_start: 0.3306 (OUTLIER) cc_final: 0.2585 (p) REVERT: B 133 TYR cc_start: 0.1714 (OUTLIER) cc_final: 0.1212 (t80) REVERT: B 274 GLU cc_start: 0.1700 (OUTLIER) cc_final: 0.1030 (mt-10) REVERT: B 282 LEU cc_start: 0.1213 (OUTLIER) cc_final: 0.0528 (tt) REVERT: B 284 ASN cc_start: 0.2575 (OUTLIER) cc_final: -0.0639 (m-40) REVERT: B 309 ARG cc_start: 0.3968 (OUTLIER) cc_final: 0.1776 (mmm160) REVERT: C 1 MET cc_start: 0.2692 (mmt) cc_final: 0.0830 (ttp) REVERT: C 77 GLU cc_start: 0.0732 (OUTLIER) cc_final: 0.0130 (pp20) REVERT: C 181 TRP cc_start: 0.2201 (OUTLIER) cc_final: 0.1603 (m-10) REVERT: C 261 LYS cc_start: 0.2786 (tptt) cc_final: 0.2109 (tptp) REVERT: C 276 VAL cc_start: 0.0223 (OUTLIER) cc_final: -0.0542 (t) REVERT: C 362 LYS cc_start: 0.2081 (OUTLIER) cc_final: 0.0064 (tmmt) outliers start: 44 outliers final: 29 residues processed: 99 average time/residue: 0.4035 time to fit residues: 53.3877 Evaluate side-chains 92 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 50 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 0.0370 chunk 78 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 148 ASN C 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2534 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 6750 Z= 0.368 Angle : 0.898 11.090 9128 Z= 0.489 Chirality : 0.047 0.170 1026 Planarity : 0.008 0.088 1198 Dihedral : 11.838 62.957 1012 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.71 % Favored : 85.94 % Rotamer: Outliers : 7.92 % Allowed : 14.66 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.26), residues: 868 helix: -2.05 (0.27), residues: 301 sheet: -3.06 (0.45), residues: 100 loop : -2.37 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 181 HIS 0.006 0.001 HIS B 0 PHE 0.035 0.003 PHE C 249 TYR 0.027 0.003 TYR C 286 ARG 0.008 0.001 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 53 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: -0.1204 (OUTLIER) cc_final: -0.2833 (pmt) REVERT: B 124 ASP cc_start: 0.1691 (OUTLIER) cc_final: 0.1274 (m-30) REVERT: B 132 THR cc_start: 0.3472 (OUTLIER) cc_final: 0.2805 (p) REVERT: B 133 TYR cc_start: 0.2094 (OUTLIER) cc_final: 0.1683 (t80) REVERT: B 213 GLU cc_start: 0.3433 (OUTLIER) cc_final: 0.2573 (tp30) REVERT: B 220 GLU cc_start: 0.3531 (OUTLIER) cc_final: 0.3174 (tt0) REVERT: B 274 GLU cc_start: 0.1547 (OUTLIER) cc_final: 0.1000 (mt-10) REVERT: B 282 LEU cc_start: 0.1208 (OUTLIER) cc_final: 0.0329 (tt) REVERT: B 284 ASN cc_start: 0.2034 (OUTLIER) cc_final: -0.0912 (m110) REVERT: B 309 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.0351 (mpt180) REVERT: B 360 MET cc_start: 0.1805 (ptt) cc_final: 0.0494 (mmt) REVERT: C 1 MET cc_start: 0.2948 (mmt) cc_final: 0.0879 (ttp) REVERT: C 23 VAL cc_start: 0.4514 (OUTLIER) cc_final: 0.4265 (t) REVERT: C 36 MET cc_start: 0.2471 (OUTLIER) cc_final: 0.1925 (tpt) REVERT: C 85 ARG cc_start: 0.4049 (mtm180) cc_final: 0.0045 (ttp-170) REVERT: C 86 ASP cc_start: 0.1498 (OUTLIER) cc_final: 0.1072 (m-30) REVERT: C 181 TRP cc_start: 0.1898 (OUTLIER) cc_final: 0.1331 (m-10) REVERT: C 261 LYS cc_start: 0.2880 (tptt) cc_final: 0.1420 (tptp) REVERT: C 276 VAL cc_start: 0.0080 (OUTLIER) cc_final: -0.0685 (t) REVERT: C 362 LYS cc_start: 0.2194 (OUTLIER) cc_final: 0.0291 (tmmt) outliers start: 54 outliers final: 32 residues processed: 104 average time/residue: 0.4127 time to fit residues: 56.8801 Evaluate side-chains 97 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 49 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 41 optimal weight: 0.0770 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2527 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 6750 Z= 0.308 Angle : 0.778 7.256 9128 Z= 0.425 Chirality : 0.045 0.160 1026 Planarity : 0.006 0.070 1198 Dihedral : 11.229 62.281 1002 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.33 % Favored : 87.44 % Rotamer: Outliers : 8.21 % Allowed : 16.13 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.26), residues: 868 helix: -1.73 (0.29), residues: 291 sheet: -3.09 (0.50), residues: 90 loop : -2.53 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 181 HIS 0.005 0.001 HIS B 0 PHE 0.024 0.002 PHE B 249 TYR 0.020 0.002 TYR B 408 ARG 0.006 0.001 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 51 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: -0.1546 (OUTLIER) cc_final: -0.3068 (pmt) REVERT: B 58 ARG cc_start: 0.2929 (OUTLIER) cc_final: -0.1622 (mmt-90) REVERT: B 124 ASP cc_start: 0.1478 (OUTLIER) cc_final: 0.0853 (m-30) REVERT: B 132 THR cc_start: 0.3471 (OUTLIER) cc_final: 0.2776 (p) REVERT: B 133 TYR cc_start: 0.2216 (OUTLIER) cc_final: 0.1793 (t80) REVERT: B 155 HIS cc_start: 0.5501 (OUTLIER) cc_final: 0.4700 (m90) REVERT: B 213 GLU cc_start: 0.3233 (OUTLIER) cc_final: 0.2848 (tp30) REVERT: B 274 GLU cc_start: 0.1486 (OUTLIER) cc_final: 0.0890 (mt-10) REVERT: B 282 LEU cc_start: 0.0917 (OUTLIER) cc_final: 0.0295 (tt) REVERT: B 284 ASN cc_start: 0.1788 (OUTLIER) cc_final: -0.1937 (p0) REVERT: B 309 ARG cc_start: 0.4563 (OUTLIER) cc_final: 0.3962 (mmm-85) REVERT: C 1 MET cc_start: 0.2830 (mmt) cc_final: 0.0767 (ttp) REVERT: C 23 VAL cc_start: 0.4279 (OUTLIER) cc_final: 0.4073 (t) REVERT: C 36 MET cc_start: 0.2449 (OUTLIER) cc_final: 0.1991 (tpt) REVERT: C 85 ARG cc_start: 0.4098 (mtm180) cc_final: 0.1148 (ttp-170) REVERT: C 86 ASP cc_start: 0.1596 (OUTLIER) cc_final: 0.1192 (m-30) REVERT: C 155 HIS cc_start: 0.4929 (OUTLIER) cc_final: 0.3484 (m90) REVERT: C 181 TRP cc_start: 0.2169 (OUTLIER) cc_final: 0.1714 (m-10) REVERT: C 261 LYS cc_start: 0.2901 (tptt) cc_final: 0.1399 (tptp) REVERT: C 276 VAL cc_start: 0.0403 (OUTLIER) cc_final: -0.0417 (t) REVERT: C 362 LYS cc_start: 0.2444 (OUTLIER) cc_final: 0.0446 (tmmt) outliers start: 56 outliers final: 35 residues processed: 105 average time/residue: 0.3994 time to fit residues: 56.1990 Evaluate side-chains 103 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 50 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2594 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 6750 Z= 0.341 Angle : 0.810 7.743 9128 Z= 0.441 Chirality : 0.045 0.162 1026 Planarity : 0.007 0.082 1198 Dihedral : 11.150 62.813 1000 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.52 % Favored : 85.25 % Rotamer: Outliers : 10.12 % Allowed : 16.42 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.25), residues: 868 helix: -1.75 (0.29), residues: 291 sheet: -3.41 (0.45), residues: 90 loop : -2.75 (0.24), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 181 HIS 0.006 0.001 HIS B 0 PHE 0.026 0.002 PHE B 249 TYR 0.021 0.002 TYR B 408 ARG 0.006 0.001 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 50 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 TYR cc_start: 0.3515 (OUTLIER) cc_final: 0.1268 (t80) REVERT: B 10 ARG cc_start: 0.3508 (OUTLIER) cc_final: 0.0111 (tpt170) REVERT: B 36 MET cc_start: -0.1631 (OUTLIER) cc_final: -0.3060 (pmt) REVERT: B 58 ARG cc_start: 0.3065 (OUTLIER) cc_final: -0.1574 (mmt-90) REVERT: B 124 ASP cc_start: 0.1622 (OUTLIER) cc_final: 0.1272 (m-30) REVERT: B 132 THR cc_start: 0.3343 (OUTLIER) cc_final: 0.2616 (p) REVERT: B 133 TYR cc_start: 0.2206 (OUTLIER) cc_final: 0.1799 (t80) REVERT: B 155 HIS cc_start: 0.5549 (OUTLIER) cc_final: 0.4709 (m90) REVERT: B 213 GLU cc_start: 0.3149 (OUTLIER) cc_final: 0.2747 (tp30) REVERT: B 220 GLU cc_start: 0.3540 (OUTLIER) cc_final: 0.3228 (tt0) REVERT: B 274 GLU cc_start: 0.1666 (OUTLIER) cc_final: 0.1303 (mt-10) REVERT: B 282 LEU cc_start: 0.1005 (OUTLIER) cc_final: 0.0321 (tt) REVERT: B 284 ASN cc_start: 0.1870 (OUTLIER) cc_final: -0.1816 (p0) REVERT: B 309 ARG cc_start: 0.4916 (OUTLIER) cc_final: 0.3807 (mmm-85) REVERT: B 360 MET cc_start: 0.1518 (ptt) cc_final: 0.0070 (mmt) REVERT: B 431 TYR cc_start: 0.6042 (m-80) cc_final: 0.5024 (m-80) REVERT: C 1 MET cc_start: 0.2755 (mmt) cc_final: 0.2311 (mmt) REVERT: C 23 VAL cc_start: 0.4370 (OUTLIER) cc_final: 0.4063 (t) REVERT: C 36 MET cc_start: 0.2553 (OUTLIER) cc_final: 0.2013 (tpt) REVERT: C 85 ARG cc_start: 0.3983 (mtm180) cc_final: 0.0061 (ttp-170) REVERT: C 86 ASP cc_start: 0.1765 (OUTLIER) cc_final: 0.1353 (m-30) REVERT: C 155 HIS cc_start: 0.5161 (OUTLIER) cc_final: 0.3605 (m90) REVERT: C 181 TRP cc_start: 0.2242 (OUTLIER) cc_final: 0.1716 (m-10) REVERT: C 205 GLU cc_start: 0.0845 (OUTLIER) cc_final: 0.0216 (tp30) REVERT: C 261 LYS cc_start: 0.3103 (tptt) cc_final: 0.1525 (tptp) REVERT: C 274 GLU cc_start: 0.1169 (OUTLIER) cc_final: 0.0767 (mm-30) REVERT: C 276 VAL cc_start: 0.0250 (OUTLIER) cc_final: -0.0708 (m) REVERT: C 362 LYS cc_start: 0.2578 (OUTLIER) cc_final: 0.1623 (tmtt) outliers start: 69 outliers final: 37 residues processed: 112 average time/residue: 0.4042 time to fit residues: 60.3277 Evaluate side-chains 108 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 48 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 TYR Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2553 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 6750 Z= 0.270 Angle : 0.723 6.657 9128 Z= 0.394 Chirality : 0.044 0.158 1026 Planarity : 0.006 0.069 1198 Dihedral : 10.588 63.328 998 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.98 % Favored : 87.90 % Rotamer: Outliers : 9.38 % Allowed : 17.30 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.25), residues: 868 helix: -1.66 (0.29), residues: 302 sheet: -3.57 (0.45), residues: 88 loop : -2.67 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 303 HIS 0.005 0.001 HIS B 0 PHE 0.023 0.002 PHE B 249 TYR 0.018 0.002 TYR B 408 ARG 0.004 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 49 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 TYR cc_start: 0.3839 (OUTLIER) cc_final: 0.1588 (t80) REVERT: B 10 ARG cc_start: 0.3553 (OUTLIER) cc_final: 0.0041 (tpt170) REVERT: B 36 MET cc_start: -0.1617 (OUTLIER) cc_final: -0.3023 (pmt) REVERT: B 58 ARG cc_start: 0.2879 (OUTLIER) cc_final: -0.1584 (mmt-90) REVERT: B 132 THR cc_start: 0.3098 (OUTLIER) cc_final: 0.2429 (p) REVERT: B 155 HIS cc_start: 0.5528 (OUTLIER) cc_final: 0.4662 (m90) REVERT: B 213 GLU cc_start: 0.3215 (OUTLIER) cc_final: 0.2890 (tp30) REVERT: B 220 GLU cc_start: 0.2989 (OUTLIER) cc_final: 0.2572 (tt0) REVERT: B 263 GLU cc_start: 0.2591 (OUTLIER) cc_final: 0.1876 (tt0) REVERT: B 284 ASN cc_start: 0.1615 (OUTLIER) cc_final: -0.1760 (p0) REVERT: B 309 ARG cc_start: 0.4669 (OUTLIER) cc_final: 0.3519 (mmm-85) REVERT: B 360 MET cc_start: 0.1947 (ptt) cc_final: 0.0223 (mmt) REVERT: B 431 TYR cc_start: 0.5980 (m-80) cc_final: 0.5048 (m-80) REVERT: C 1 MET cc_start: 0.2793 (mmt) cc_final: 0.2331 (mmt) REVERT: C 85 ARG cc_start: 0.4131 (mtm180) cc_final: 0.0110 (ttp-170) REVERT: C 86 ASP cc_start: 0.1744 (OUTLIER) cc_final: 0.1454 (m-30) REVERT: C 155 HIS cc_start: 0.5090 (OUTLIER) cc_final: 0.3550 (m90) REVERT: C 181 TRP cc_start: 0.2269 (OUTLIER) cc_final: 0.1791 (m-10) REVERT: C 205 GLU cc_start: 0.0754 (OUTLIER) cc_final: 0.0213 (tp30) REVERT: C 276 VAL cc_start: 0.0329 (OUTLIER) cc_final: -0.0421 (t) REVERT: C 342 LEU cc_start: 0.2560 (OUTLIER) cc_final: 0.2095 (tp) outliers start: 64 outliers final: 41 residues processed: 104 average time/residue: 0.4301 time to fit residues: 59.6312 Evaluate side-chains 106 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 48 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 TYR Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.0170 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2580 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 6750 Z= 0.290 Angle : 0.736 7.273 9128 Z= 0.400 Chirality : 0.044 0.155 1026 Planarity : 0.006 0.074 1198 Dihedral : 10.271 61.713 992 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.71 % Favored : 85.94 % Rotamer: Outliers : 8.94 % Allowed : 17.60 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.26), residues: 868 helix: -1.60 (0.29), residues: 302 sheet: -3.57 (0.42), residues: 98 loop : -2.66 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 300 HIS 0.004 0.001 HIS B 0 PHE 0.029 0.002 PHE B 242 TYR 0.018 0.002 TYR B 408 ARG 0.006 0.001 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 51 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 TYR cc_start: 0.4019 (OUTLIER) cc_final: 0.2102 (t80) REVERT: B 10 ARG cc_start: 0.3204 (OUTLIER) cc_final: -0.0061 (tpt170) REVERT: B 36 MET cc_start: -0.1614 (OUTLIER) cc_final: -0.2994 (pmt) REVERT: B 58 ARG cc_start: 0.2909 (OUTLIER) cc_final: -0.1664 (mmt90) REVERT: B 132 THR cc_start: 0.3170 (OUTLIER) cc_final: 0.2611 (p) REVERT: B 155 HIS cc_start: 0.5600 (OUTLIER) cc_final: 0.4723 (m90) REVERT: B 213 GLU cc_start: 0.3139 (OUTLIER) cc_final: 0.2879 (tp30) REVERT: B 220 GLU cc_start: 0.3081 (OUTLIER) cc_final: 0.2649 (tt0) REVERT: B 284 ASN cc_start: 0.1874 (OUTLIER) cc_final: -0.1317 (m110) REVERT: B 309 ARG cc_start: 0.4630 (OUTLIER) cc_final: 0.3263 (mmm-85) REVERT: B 360 MET cc_start: 0.1901 (ptt) cc_final: 0.0151 (mmt) REVERT: B 431 TYR cc_start: 0.6020 (m-80) cc_final: 0.5093 (m-80) REVERT: C 1 MET cc_start: 0.2748 (mmt) cc_final: 0.2306 (mmt) REVERT: C 82 TYR cc_start: 0.1712 (m-80) cc_final: 0.1069 (m-80) REVERT: C 85 ARG cc_start: 0.4027 (mtm180) cc_final: 0.0241 (ttp-170) REVERT: C 86 ASP cc_start: 0.1559 (OUTLIER) cc_final: 0.1189 (m-30) REVERT: C 155 HIS cc_start: 0.5138 (OUTLIER) cc_final: 0.3667 (m90) REVERT: C 181 TRP cc_start: 0.2156 (OUTLIER) cc_final: 0.1667 (m-10) REVERT: C 205 GLU cc_start: 0.0878 (OUTLIER) cc_final: 0.0301 (tp30) REVERT: C 274 GLU cc_start: 0.0928 (OUTLIER) cc_final: 0.0608 (mm-30) REVERT: C 276 VAL cc_start: 0.0400 (OUTLIER) cc_final: -0.0493 (m) REVERT: C 342 LEU cc_start: 0.2671 (OUTLIER) cc_final: 0.2097 (tp) outliers start: 61 outliers final: 42 residues processed: 103 average time/residue: 0.4172 time to fit residues: 56.6269 Evaluate side-chains 108 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 49 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 TYR Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2708 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.186 6750 Z= 0.420 Angle : 0.892 8.958 9128 Z= 0.486 Chirality : 0.047 0.165 1026 Planarity : 0.008 0.086 1198 Dihedral : 11.052 61.151 992 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.98 % Favored : 84.68 % Rotamer: Outliers : 9.68 % Allowed : 17.01 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.25), residues: 868 helix: -1.89 (0.28), residues: 287 sheet: -3.78 (0.43), residues: 88 loop : -2.88 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 181 HIS 0.008 0.002 HIS B 0 PHE 0.037 0.003 PHE B 165 TYR 0.022 0.002 TYR B 408 ARG 0.008 0.001 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 50 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 TYR cc_start: 0.4297 (OUTLIER) cc_final: 0.2259 (t80) REVERT: B 10 ARG cc_start: 0.3285 (OUTLIER) cc_final: -0.0097 (tpt170) REVERT: B 58 ARG cc_start: 0.3327 (OUTLIER) cc_final: -0.1176 (mmt-90) REVERT: B 124 ASP cc_start: 0.1593 (OUTLIER) cc_final: 0.1273 (t70) REVERT: B 132 THR cc_start: 0.3470 (OUTLIER) cc_final: 0.2905 (p) REVERT: B 133 TYR cc_start: 0.2540 (OUTLIER) cc_final: 0.2133 (t80) REVERT: B 155 HIS cc_start: 0.5680 (OUTLIER) cc_final: 0.4986 (m90) REVERT: B 213 GLU cc_start: 0.3266 (OUTLIER) cc_final: 0.2842 (tp30) REVERT: B 220 GLU cc_start: 0.3725 (OUTLIER) cc_final: 0.3406 (tt0) REVERT: B 284 ASN cc_start: 0.2184 (OUTLIER) cc_final: -0.1689 (p0) REVERT: B 309 ARG cc_start: 0.5051 (OUTLIER) cc_final: 0.0820 (mpt180) REVERT: B 360 MET cc_start: 0.1938 (ptt) cc_final: -0.0006 (mmt) REVERT: B 431 TYR cc_start: 0.6241 (m-80) cc_final: 0.5566 (m-80) REVERT: C 1 MET cc_start: 0.2835 (mmt) cc_final: 0.2345 (mmt) REVERT: C 51 LEU cc_start: 0.1616 (OUTLIER) cc_final: -0.0468 (mt) REVERT: C 82 TYR cc_start: 0.1806 (m-80) cc_final: 0.1124 (m-80) REVERT: C 85 ARG cc_start: 0.4165 (mtm180) cc_final: 0.1104 (ttp-170) REVERT: C 86 ASP cc_start: 0.1471 (OUTLIER) cc_final: 0.0990 (m-30) REVERT: C 181 TRP cc_start: 0.2176 (OUTLIER) cc_final: 0.1626 (m-10) REVERT: C 205 GLU cc_start: 0.0923 (OUTLIER) cc_final: 0.0518 (tp30) REVERT: C 276 VAL cc_start: 0.0261 (OUTLIER) cc_final: -0.0621 (m) outliers start: 66 outliers final: 42 residues processed: 108 average time/residue: 0.4056 time to fit residues: 58.2105 Evaluate side-chains 108 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 50 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 TYR Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2628 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 6750 Z= 0.291 Angle : 0.738 6.601 9128 Z= 0.401 Chirality : 0.044 0.162 1026 Planarity : 0.006 0.069 1198 Dihedral : 10.485 60.409 992 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.71 % Favored : 86.06 % Rotamer: Outliers : 8.06 % Allowed : 18.18 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.25), residues: 868 helix: -1.77 (0.28), residues: 298 sheet: -3.95 (0.41), residues: 98 loop : -2.85 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 300 HIS 0.006 0.001 HIS B 0 PHE 0.026 0.002 PHE B 165 TYR 0.018 0.002 TYR B 408 ARG 0.003 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 52 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 TYR cc_start: 0.4137 (OUTLIER) cc_final: 0.2079 (t80) REVERT: B 10 ARG cc_start: 0.3492 (OUTLIER) cc_final: 0.0086 (tpt170) REVERT: B 36 MET cc_start: -0.2042 (OUTLIER) cc_final: -0.3336 (pmt) REVERT: B 58 ARG cc_start: 0.3033 (OUTLIER) cc_final: -0.1396 (mmt-90) REVERT: B 132 THR cc_start: 0.3323 (OUTLIER) cc_final: 0.2733 (p) REVERT: B 155 HIS cc_start: 0.5476 (OUTLIER) cc_final: 0.4663 (m90) REVERT: B 220 GLU cc_start: 0.3285 (OUTLIER) cc_final: 0.2855 (tt0) REVERT: B 284 ASN cc_start: 0.1586 (OUTLIER) cc_final: -0.2109 (p0) REVERT: B 309 ARG cc_start: 0.4690 (OUTLIER) cc_final: 0.0846 (mpt180) REVERT: B 360 MET cc_start: 0.1892 (ptt) cc_final: 0.0029 (mmt) REVERT: C 1 MET cc_start: 0.2950 (mmt) cc_final: 0.2446 (mmt) REVERT: C 82 TYR cc_start: 0.1864 (m-80) cc_final: 0.1293 (m-80) REVERT: C 85 ARG cc_start: 0.4032 (mtm180) cc_final: 0.0433 (ttp-170) REVERT: C 86 ASP cc_start: 0.1350 (OUTLIER) cc_final: 0.1020 (m-30) REVERT: C 181 TRP cc_start: 0.2135 (OUTLIER) cc_final: 0.1595 (m-10) REVERT: C 205 GLU cc_start: 0.0660 (OUTLIER) cc_final: 0.0213 (tp30) REVERT: C 276 VAL cc_start: 0.0466 (OUTLIER) cc_final: -0.0441 (m) outliers start: 55 outliers final: 40 residues processed: 100 average time/residue: 0.4239 time to fit residues: 56.1021 Evaluate side-chains 105 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 52 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 TYR Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 278 TYR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 78 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 ASN C 18 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2427 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6750 Z= 0.175 Angle : 0.604 5.616 9128 Z= 0.324 Chirality : 0.042 0.140 1026 Planarity : 0.005 0.065 1198 Dihedral : 9.301 59.501 989 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.53 % Favored : 91.24 % Rotamer: Outliers : 3.96 % Allowed : 22.14 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.26), residues: 868 helix: -1.30 (0.29), residues: 310 sheet: -3.68 (0.42), residues: 99 loop : -2.73 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 300 HIS 0.003 0.001 HIS B 0 PHE 0.020 0.002 PHE B 165 TYR 0.017 0.001 TYR B 408 ARG 0.003 0.001 ARG B 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 49 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 ARG cc_start: 0.3196 (OUTLIER) cc_final: 0.0401 (tpt170) REVERT: B 36 MET cc_start: -0.1738 (OUTLIER) cc_final: -0.3266 (pmt) REVERT: B 132 THR cc_start: 0.3373 (OUTLIER) cc_final: 0.2934 (p) REVERT: B 155 HIS cc_start: 0.5085 (OUTLIER) cc_final: 0.4099 (m90) REVERT: B 263 GLU cc_start: 0.2447 (OUTLIER) cc_final: 0.2012 (tt0) REVERT: B 284 ASN cc_start: 0.1547 (OUTLIER) cc_final: -0.1243 (m-40) REVERT: B 309 ARG cc_start: 0.4099 (OUTLIER) cc_final: 0.3402 (mmm-85) REVERT: B 360 MET cc_start: 0.1848 (ptt) cc_final: 0.0024 (mmt) REVERT: C 1 MET cc_start: 0.2877 (mmt) cc_final: 0.2391 (mmt) REVERT: C 36 MET cc_start: 0.2084 (OUTLIER) cc_final: 0.1290 (tpt) REVERT: C 82 TYR cc_start: 0.1835 (m-80) cc_final: 0.0729 (m-80) REVERT: C 181 TRP cc_start: 0.2214 (OUTLIER) cc_final: 0.1512 (m-10) outliers start: 27 outliers final: 17 residues processed: 73 average time/residue: 0.4332 time to fit residues: 41.9086 Evaluate side-chains 74 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 48 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 424 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 ASN C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5389 r_free = 0.5389 target = 0.355624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.346326 restraints weight = 272378.618| |-----------------------------------------------------------------------------| r_work (start): 0.5290 rms_B_bonded: 6.59 r_work (final): 0.5290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2715 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6750 Z= 0.247 Angle : 0.660 5.999 9128 Z= 0.357 Chirality : 0.042 0.157 1026 Planarity : 0.006 0.069 1198 Dihedral : 9.460 57.292 988 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.10 % Favored : 87.67 % Rotamer: Outliers : 4.25 % Allowed : 21.99 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.26), residues: 868 helix: -1.37 (0.29), residues: 313 sheet: -3.87 (0.42), residues: 99 loop : -2.74 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 300 HIS 0.005 0.001 HIS B 0 PHE 0.022 0.002 PHE B 165 TYR 0.015 0.001 TYR B 408 ARG 0.003 0.000 ARG B 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.63 seconds wall clock time: 54 minutes 18.38 seconds (3258.38 seconds total)