Starting phenix.real_space_refine on Thu May 9 13:03:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/05_2024/8uoy_42441.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/05_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_42441/05_2024/8uoy_42441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/05_2024/8uoy_42441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/05_2024/8uoy_42441.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoy_42441/05_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 6.32, per 1000 atoms: 0.48 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: 10.23 Conformation dependent library (CDL) restraints added in 1.4 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: 1.03 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: 4.55 Time building geometry restraints manager: 10.66 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: 5349 16.79 - 33.59: 568 33.59 - 50.38: 182 50.38 - 67.17: 97 67.17 - 83.97: 16 Dihedral angle restraints: 6212 sinusoidal: 3390 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 6209 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: 0.010 Normalize map: mean=0, sd=1: 0.410 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: 0.170 Extract box with map and model: 2.760 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 44.390 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.060 ------------------------------------------------------------------------------- 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 : 1.008 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: 0.4385 time to fit residues: 68.3639 Evaluate side-chains 97 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 61 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 18 ASN ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2376 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 6750 Z= 0.299 Angle : 0.874 10.837 9128 Z= 0.475 Chirality : 0.047 0.166 1026 Planarity : 0.006 0.068 1198 Dihedral : 12.648 65.189 1029 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.60 % Favored : 88.94 % Rotamer: Outliers : 6.60 % Allowed : 12.76 % Favored : 80.65 % 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: -3.42 (0.25), residues: 868 helix: -2.28 (0.26), residues: 293 sheet: -2.90 (0.45), residues: 102 loop : -2.09 (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 103 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 58 time to evaluate : 0.974 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: B 36 MET cc_start: -0.0875 (OUTLIER) cc_final: -0.3105 (pmt) REVERT: B 124 ASP cc_start: 0.1066 (OUTLIER) cc_final: 0.0687 (m-30) REVERT: B 126 LEU cc_start: 0.0062 (OUTLIER) cc_final: -0.1594 (mt) REVERT: B 132 THR cc_start: 0.3320 (OUTLIER) cc_final: 0.2606 (p) REVERT: B 133 TYR cc_start: 0.1724 (OUTLIER) cc_final: 0.1234 (t80) REVERT: B 274 GLU cc_start: 0.1682 (OUTLIER) cc_final: 0.1006 (mt-10) REVERT: B 282 LEU cc_start: 0.1216 (OUTLIER) cc_final: 0.0534 (tt) REVERT: B 284 ASN cc_start: 0.2571 (OUTLIER) cc_final: -0.0648 (m-40) REVERT: B 309 ARG cc_start: 0.4004 (OUTLIER) cc_final: 0.1775 (mmm160) REVERT: C 1 MET cc_start: 0.2685 (mmt) cc_final: 0.0817 (ttp) REVERT: C 36 MET cc_start: 0.2412 (OUTLIER) cc_final: 0.1735 (tpp) REVERT: C 77 GLU cc_start: 0.0732 (OUTLIER) cc_final: -0.0095 (pp20) REVERT: C 181 TRP cc_start: 0.2207 (OUTLIER) cc_final: 0.1593 (m-10) REVERT: C 261 LYS cc_start: 0.2783 (tptt) cc_final: 0.2101 (tptp) REVERT: C 276 VAL cc_start: 0.0220 (OUTLIER) cc_final: -0.0542 (t) REVERT: C 362 LYS cc_start: 0.2094 (OUTLIER) cc_final: 0.0075 (tmmt) outliers start: 45 outliers final: 29 residues processed: 100 average time/residue: 0.4285 time to fit residues: 57.4587 Evaluate side-chains 95 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 52 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 65 GLN 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: 5.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2518 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 6750 Z= 0.350 Angle : 0.873 11.051 9128 Z= 0.475 Chirality : 0.047 0.167 1026 Planarity : 0.008 0.085 1198 Dihedral : 11.751 62.851 1012 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.13 % Favored : 86.52 % Rotamer: Outliers : 8.06 % Allowed : 14.66 % Favored : 77.27 % 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: -1.99 (0.27), residues: 303 sheet: -3.02 (0.45), residues: 100 loop : -2.32 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 181 HIS 0.006 0.002 HIS B 0 PHE 0.035 0.003 PHE C 249 TYR 0.025 0.002 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 109 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 54 time to evaluate : 0.987 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: B 36 MET cc_start: -0.1274 (OUTLIER) cc_final: -0.2861 (pmt) REVERT: B 124 ASP cc_start: 0.1900 (OUTLIER) cc_final: 0.1481 (m-30) REVERT: B 132 THR cc_start: 0.3552 (OUTLIER) cc_final: 0.2844 (p) REVERT: B 133 TYR cc_start: 0.2081 (OUTLIER) cc_final: 0.1670 (t80) REVERT: B 213 GLU cc_start: 0.3419 (OUTLIER) cc_final: 0.2573 (tp30) REVERT: B 220 GLU cc_start: 0.3567 (OUTLIER) cc_final: 0.3206 (tt0) REVERT: B 274 GLU cc_start: 0.1658 (OUTLIER) cc_final: 0.1116 (mt-10) REVERT: B 282 LEU cc_start: 0.1183 (OUTLIER) cc_final: 0.0307 (tt) REVERT: B 284 ASN cc_start: 0.1991 (OUTLIER) cc_final: -0.1359 (m110) REVERT: B 309 ARG cc_start: 0.4646 (OUTLIER) cc_final: 0.0340 (mpt180) REVERT: B 360 MET cc_start: 0.1647 (ptt) cc_final: 0.0542 (mmt) REVERT: B 431 TYR cc_start: 0.5556 (m-80) cc_final: 0.4795 (m-80) REVERT: C 1 MET cc_start: 0.2919 (mmt) cc_final: 0.0856 (ttp) REVERT: C 23 VAL cc_start: 0.4548 (OUTLIER) cc_final: 0.4262 (t) REVERT: C 36 MET cc_start: 0.2440 (OUTLIER) cc_final: 0.2009 (tpt) REVERT: C 85 ARG cc_start: 0.4102 (mtm180) cc_final: 0.0290 (ttp80) REVERT: C 86 ASP cc_start: 0.1597 (OUTLIER) cc_final: 0.1173 (m-30) REVERT: C 155 HIS cc_start: 0.4803 (OUTLIER) cc_final: 0.3865 (m90) REVERT: C 181 TRP cc_start: 0.2089 (OUTLIER) cc_final: 0.1496 (m-10) REVERT: C 261 LYS cc_start: 0.2867 (tptt) cc_final: 0.1364 (tptp) REVERT: C 276 VAL cc_start: 0.0235 (OUTLIER) cc_final: -0.0546 (t) REVERT: C 362 LYS cc_start: 0.2131 (OUTLIER) cc_final: 0.0257 (tmmt) outliers start: 55 outliers final: 31 residues processed: 106 average time/residue: 0.4143 time to fit residues: 58.4497 Evaluate side-chains 97 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 49 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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: 0.2521 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 6750 Z= 0.306 Angle : 0.778 7.611 9128 Z= 0.425 Chirality : 0.045 0.160 1026 Planarity : 0.006 0.070 1198 Dihedral : 11.092 61.199 1000 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.56 % Favored : 87.21 % Rotamer: Outliers : 8.06 % Allowed : 16.28 % 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: -3.41 (0.26), residues: 868 helix: -1.73 (0.29), residues: 291 sheet: -3.06 (0.49), residues: 90 loop : -2.50 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 181 HIS 0.011 0.002 HIS C 155 PHE 0.024 0.002 PHE B 249 TYR 0.021 0.002 TYR B 408 ARG 0.006 0.000 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: 55 poor density : 52 time to evaluate : 0.965 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: B 36 MET cc_start: -0.1433 (OUTLIER) cc_final: -0.2933 (pmt) REVERT: B 58 ARG cc_start: 0.2928 (OUTLIER) cc_final: -0.1588 (mmt-90) REVERT: B 124 ASP cc_start: 0.1657 (OUTLIER) cc_final: 0.1230 (m-30) REVERT: B 132 THR cc_start: 0.3533 (OUTLIER) cc_final: 0.2814 (p) REVERT: B 133 TYR cc_start: 0.2154 (OUTLIER) cc_final: 0.1746 (t80) REVERT: B 155 HIS cc_start: 0.5500 (OUTLIER) cc_final: 0.4717 (m90) REVERT: B 213 GLU cc_start: 0.3227 (OUTLIER) cc_final: 0.2795 (tp30) REVERT: B 274 GLU cc_start: 0.1567 (OUTLIER) cc_final: 0.0972 (mt-10) REVERT: B 282 LEU cc_start: 0.0927 (OUTLIER) cc_final: 0.0300 (tt) REVERT: B 284 ASN cc_start: 0.1700 (OUTLIER) cc_final: -0.2006 (p0) REVERT: B 309 ARG cc_start: 0.4635 (OUTLIER) cc_final: 0.4016 (mmm-85) REVERT: B 360 MET cc_start: 0.2118 (ptt) cc_final: 0.0560 (mmt) REVERT: C 1 MET cc_start: 0.2810 (mmt) cc_final: 0.0749 (ttp) REVERT: C 23 VAL cc_start: 0.4620 (OUTLIER) cc_final: 0.4269 (t) REVERT: C 36 MET cc_start: 0.2497 (OUTLIER) cc_final: 0.2005 (tpt) REVERT: C 85 ARG cc_start: 0.4080 (mtm180) cc_final: 0.1147 (ttp-170) REVERT: C 86 ASP cc_start: 0.1607 (OUTLIER) cc_final: 0.1199 (m-30) REVERT: C 181 TRP cc_start: 0.2160 (OUTLIER) cc_final: 0.1660 (m-10) REVERT: C 261 LYS cc_start: 0.2873 (tptt) cc_final: 0.1560 (tptp) REVERT: C 276 VAL cc_start: 0.0345 (OUTLIER) cc_final: -0.0498 (t) REVERT: C 362 LYS cc_start: 0.2380 (OUTLIER) cc_final: 0.0395 (tmmt) outliers start: 55 outliers final: 34 residues processed: 105 average time/residue: 0.4197 time to fit residues: 59.2895 Evaluate side-chains 101 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 50 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.2524 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 6750 Z= 0.275 Angle : 0.725 6.671 9128 Z= 0.395 Chirality : 0.044 0.155 1026 Planarity : 0.006 0.075 1198 Dihedral : 10.738 61.104 1000 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.90 % Favored : 86.98 % Rotamer: Outliers : 9.09 % Allowed : 16.72 % Favored : 74.19 % 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: -3.41 (0.26), residues: 868 helix: -1.54 (0.30), residues: 286 sheet: -3.29 (0.47), residues: 90 loop : -2.57 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 300 HIS 0.005 0.001 HIS B 0 PHE 0.023 0.002 PHE B 249 TYR 0.021 0.002 TYR B 408 ARG 0.005 0.000 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 111 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 49 time to evaluate : 1.216 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: 0.3381 (OUTLIER) cc_final: 0.1251 (t80) REVERT: B 10 ARG cc_start: 0.3433 (OUTLIER) cc_final: 0.0184 (tpt170) REVERT: B 36 MET cc_start: -0.1797 (OUTLIER) cc_final: -0.3172 (pmt) REVERT: B 58 ARG cc_start: 0.2861 (OUTLIER) cc_final: -0.1979 (mmt90) REVERT: B 124 ASP cc_start: 0.1466 (OUTLIER) cc_final: 0.1085 (m-30) REVERT: B 132 THR cc_start: 0.3282 (OUTLIER) cc_final: 0.2621 (p) REVERT: B 155 HIS cc_start: 0.5620 (OUTLIER) cc_final: 0.4707 (m90) REVERT: B 166 MET cc_start: 0.2351 (ptp) cc_final: 0.2088 (ptp) REVERT: B 213 GLU cc_start: 0.3342 (OUTLIER) cc_final: 0.2903 (tp30) REVERT: B 263 GLU cc_start: 0.2640 (OUTLIER) cc_final: 0.1972 (tt0) REVERT: B 274 GLU cc_start: 0.1591 (OUTLIER) cc_final: 0.0991 (mt-10) REVERT: B 282 LEU cc_start: 0.0631 (OUTLIER) cc_final: 0.0069 (tt) REVERT: B 284 ASN cc_start: 0.1556 (OUTLIER) cc_final: -0.2014 (p0) REVERT: B 309 ARG cc_start: 0.4788 (OUTLIER) cc_final: 0.4248 (mmm-85) REVERT: C 1 MET cc_start: 0.2511 (mmt) cc_final: 0.0572 (ttp) REVERT: C 36 MET cc_start: 0.2456 (OUTLIER) cc_final: 0.1920 (tpt) REVERT: C 85 ARG cc_start: 0.4105 (mtm180) cc_final: 0.0067 (ttp-170) REVERT: C 86 ASP cc_start: 0.1565 (OUTLIER) cc_final: 0.1241 (m-30) REVERT: C 181 TRP cc_start: 0.2340 (OUTLIER) cc_final: 0.1794 (m-10) REVERT: C 205 GLU cc_start: 0.0806 (OUTLIER) cc_final: 0.0217 (tp30) REVERT: C 274 GLU cc_start: 0.1043 (OUTLIER) cc_final: 0.0693 (mm-30) REVERT: C 276 VAL cc_start: 0.0121 (OUTLIER) cc_final: -0.0770 (m) REVERT: C 278 TYR cc_start: 0.2177 (OUTLIER) cc_final: 0.1583 (t80) REVERT: C 285 LYS cc_start: 0.4274 (tppt) cc_final: 0.3977 (ttpt) REVERT: C 362 LYS cc_start: 0.2395 (OUTLIER) cc_final: 0.0457 (tmmt) outliers start: 62 outliers final: 36 residues processed: 107 average time/residue: 0.4319 time to fit residues: 61.3590 Evaluate side-chains 105 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 48 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 68 VAL 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 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 238 ILE Chi-restraints excluded: chain B residue 239 MET 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 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 68 VAL Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 149 ILE 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 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 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: 3.9990 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.0000 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.7590 ------------------------------------------------------------------------------- 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: 0.2474 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 6750 Z= 0.228 Angle : 0.662 6.106 9128 Z= 0.360 Chirality : 0.043 0.151 1026 Planarity : 0.005 0.069 1198 Dihedral : 10.323 59.814 1000 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.83 % Favored : 89.06 % Rotamer: Outliers : 7.77 % Allowed : 18.33 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.32 (0.26), residues: 868 helix: -1.40 (0.30), residues: 297 sheet: -3.18 (0.45), residues: 100 loop : -2.56 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 300 HIS 0.004 0.001 HIS B 0 PHE 0.023 0.002 PHE B 249 TYR 0.018 0.001 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 103 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 50 time to evaluate : 1.010 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 10 ARG cc_start: 0.3581 (OUTLIER) cc_final: 0.0640 (tpt170) REVERT: B 36 MET cc_start: -0.1644 (OUTLIER) cc_final: -0.3040 (pmt) REVERT: B 58 ARG cc_start: 0.2770 (OUTLIER) cc_final: -0.1748 (mmt90) REVERT: B 124 ASP cc_start: 0.1132 (OUTLIER) cc_final: 0.0734 (m-30) REVERT: B 132 THR cc_start: 0.3062 (OUTLIER) cc_final: 0.2424 (p) REVERT: B 155 HIS cc_start: 0.5667 (OUTLIER) cc_final: 0.4718 (m90) REVERT: B 213 GLU cc_start: 0.3385 (OUTLIER) cc_final: 0.3023 (tp30) REVERT: B 263 GLU cc_start: 0.2418 (OUTLIER) cc_final: 0.1841 (tt0) REVERT: B 274 GLU cc_start: 0.1504 (OUTLIER) cc_final: 0.1100 (mt-10) REVERT: B 282 LEU cc_start: 0.0974 (OUTLIER) cc_final: 0.0769 (tp) REVERT: B 284 ASN cc_start: 0.1795 (OUTLIER) cc_final: -0.0895 (m-40) REVERT: B 309 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.3531 (mmm-85) REVERT: B 360 MET cc_start: 0.1417 (ptt) cc_final: -0.0095 (mmt) REVERT: C 1 MET cc_start: 0.2496 (mmt) cc_final: 0.2048 (mmt) REVERT: C 85 ARG cc_start: 0.4105 (mtm180) cc_final: 0.1533 (tmm-80) REVERT: C 86 ASP cc_start: 0.1451 (OUTLIER) cc_final: 0.1091 (m-30) REVERT: C 155 HIS cc_start: 0.4964 (OUTLIER) cc_final: 0.3708 (m90) REVERT: C 181 TRP cc_start: 0.2206 (OUTLIER) cc_final: 0.1678 (m-10) REVERT: C 261 LYS cc_start: 0.2898 (tptt) cc_final: 0.1132 (tptp) REVERT: C 285 LYS cc_start: 0.4211 (tppt) cc_final: 0.3898 (ttpt) REVERT: C 362 LYS cc_start: 0.2612 (OUTLIER) cc_final: 0.1629 (tmtt) REVERT: C 372 HIS cc_start: 0.2189 (OUTLIER) cc_final: 0.1700 (p-80) outliers start: 53 outliers final: 32 residues processed: 99 average time/residue: 0.4418 time to fit residues: 58.4231 Evaluate side-chains 99 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 50 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 57 SER Chi-restraints excluded: chain B residue 58 ARG 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 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 213 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 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 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 66 LYS 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 226 ILE Chi-restraints excluded: chain C residue 232 GLU 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: 10.0000 chunk 47 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 0.0870 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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: 0.2601 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 6750 Z= 0.334 Angle : 0.784 7.858 9128 Z= 0.426 Chirality : 0.045 0.159 1026 Planarity : 0.007 0.092 1198 Dihedral : 10.630 58.467 997 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.17 % Favored : 85.60 % Rotamer: Outliers : 8.80 % Allowed : 17.45 % Favored : 73.75 % 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: -3.53 (0.26), residues: 868 helix: -1.51 (0.29), residues: 291 sheet: -3.40 (0.43), residues: 98 loop : -2.70 (0.25), residues: 479 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 0.024 0.002 PHE B 249 TYR 0.018 0.002 TYR B 408 ARG 0.005 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 109 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 49 time to evaluate : 0.965 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: 0.3820 (OUTLIER) cc_final: 0.2042 (t80) REVERT: B 10 ARG cc_start: 0.3407 (OUTLIER) cc_final: 0.0097 (tpt170) REVERT: B 36 MET cc_start: -0.1638 (OUTLIER) cc_final: -0.3019 (pmt) REVERT: B 58 ARG cc_start: 0.2961 (OUTLIER) cc_final: -0.1635 (mmt-90) REVERT: B 132 THR cc_start: 0.3296 (OUTLIER) cc_final: 0.2743 (p) REVERT: B 133 TYR cc_start: 0.2231 (OUTLIER) cc_final: 0.1810 (t80) REVERT: B 155 HIS cc_start: 0.5614 (OUTLIER) cc_final: 0.4738 (m90) REVERT: B 213 GLU cc_start: 0.3226 (OUTLIER) cc_final: 0.2946 (tp30) REVERT: B 282 LEU cc_start: 0.0985 (OUTLIER) cc_final: 0.0282 (tt) REVERT: B 284 ASN cc_start: 0.1710 (OUTLIER) cc_final: -0.2080 (p0) REVERT: B 309 ARG cc_start: 0.5000 (OUTLIER) cc_final: 0.3562 (mmm-85) REVERT: B 360 MET cc_start: 0.1547 (ptt) cc_final: -0.0113 (mmt) REVERT: B 431 TYR cc_start: 0.6024 (m-80) cc_final: 0.5421 (m-80) REVERT: C 1 MET cc_start: 0.2862 (mmt) cc_final: 0.2376 (mmt) REVERT: C 82 TYR cc_start: 0.1867 (m-80) cc_final: 0.1175 (m-80) REVERT: C 85 ARG cc_start: 0.4085 (mtm180) cc_final: 0.0213 (ttp-170) REVERT: C 86 ASP cc_start: 0.1638 (OUTLIER) cc_final: 0.1220 (m-30) REVERT: C 181 TRP cc_start: 0.2163 (OUTLIER) cc_final: 0.1584 (m-10) REVERT: C 205 GLU cc_start: 0.0928 (OUTLIER) cc_final: 0.0299 (tp30) REVERT: C 274 GLU cc_start: 0.0931 (OUTLIER) cc_final: 0.0612 (mm-30) REVERT: C 276 VAL cc_start: 0.0466 (OUTLIER) cc_final: -0.0463 (m) REVERT: C 285 LYS cc_start: 0.4539 (tppt) cc_final: 0.4166 (ttpt) outliers start: 60 outliers final: 41 residues processed: 104 average time/residue: 0.4217 time to fit residues: 57.9947 Evaluate side-chains 107 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 50 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 238 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 263 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 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 146 MET 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 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 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: 4.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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: 0.2600 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 6750 Z= 0.314 Angle : 0.755 7.298 9128 Z= 0.410 Chirality : 0.044 0.160 1026 Planarity : 0.006 0.071 1198 Dihedral : 10.487 59.087 994 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.90 % Favored : 86.75 % Rotamer: Outliers : 8.65 % Allowed : 17.89 % 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: -3.58 (0.25), residues: 868 helix: -1.64 (0.28), residues: 302 sheet: -3.41 (0.46), residues: 88 loop : -2.72 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 181 HIS 0.006 0.001 HIS B 0 PHE 0.022 0.002 PHE B 249 TYR 0.018 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 111 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 52 time to evaluate : 1.029 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: B 8 TYR cc_start: 0.4016 (OUTLIER) cc_final: 0.2061 (t80) REVERT: B 10 ARG cc_start: 0.3382 (OUTLIER) cc_final: 0.0146 (tpt170) REVERT: B 36 MET cc_start: -0.1731 (OUTLIER) cc_final: -0.3199 (pmt) REVERT: B 58 ARG cc_start: 0.2915 (OUTLIER) cc_final: -0.1759 (mmt90) REVERT: B 132 THR cc_start: 0.3276 (OUTLIER) cc_final: 0.2640 (p) REVERT: B 133 TYR cc_start: 0.2259 (OUTLIER) cc_final: 0.1812 (t80) REVERT: B 155 HIS cc_start: 0.5553 (OUTLIER) cc_final: 0.4662 (m90) REVERT: B 282 LEU cc_start: 0.1017 (OUTLIER) cc_final: 0.0314 (tt) REVERT: B 284 ASN cc_start: 0.1806 (OUTLIER) cc_final: -0.1994 (p0) REVERT: B 295 MET cc_start: 0.3606 (ptp) cc_final: 0.3390 (ptp) REVERT: B 309 ARG cc_start: 0.4714 (OUTLIER) cc_final: 0.3254 (mmm-85) REVERT: B 360 MET cc_start: 0.1754 (ptt) cc_final: 0.0038 (mmt) REVERT: C 1 MET cc_start: 0.2829 (mmt) cc_final: 0.2349 (mmt) REVERT: C 82 TYR cc_start: 0.1831 (m-80) cc_final: 0.1172 (m-80) REVERT: C 85 ARG cc_start: 0.4091 (mtm180) cc_final: 0.0252 (ttp-170) REVERT: C 86 ASP cc_start: 0.1588 (OUTLIER) cc_final: 0.1227 (m-30) REVERT: C 155 HIS cc_start: 0.5052 (OUTLIER) cc_final: 0.3670 (m170) REVERT: C 181 TRP cc_start: 0.2059 (OUTLIER) cc_final: 0.1534 (m-10) REVERT: C 205 GLU cc_start: 0.0727 (OUTLIER) cc_final: 0.0185 (tp30) REVERT: C 274 GLU cc_start: 0.0805 (OUTLIER) cc_final: 0.0603 (mm-30) REVERT: C 276 VAL cc_start: 0.0199 (OUTLIER) cc_final: -0.0531 (t) REVERT: C 285 LYS cc_start: 0.4510 (tppt) cc_final: 0.4147 (ttpt) outliers start: 59 outliers final: 41 residues processed: 105 average time/residue: 0.4527 time to fit residues: 63.5855 Evaluate side-chains 109 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 52 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 215 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 263 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 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 11 GLU Chi-restraints excluded: chain C residue 24 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 146 MET 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 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: 9.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2530 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 6750 Z= 0.231 Angle : 0.656 6.129 9128 Z= 0.357 Chirality : 0.043 0.152 1026 Planarity : 0.005 0.070 1198 Dihedral : 9.930 56.918 993 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.56 % Favored : 87.21 % Rotamer: Outliers : 8.06 % Allowed : 18.33 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.41 (0.26), residues: 868 helix: -1.40 (0.29), residues: 302 sheet: -3.42 (0.45), residues: 98 loop : -2.63 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 300 HIS 0.004 0.001 HIS B 0 PHE 0.025 0.002 PHE B 242 TYR 0.015 0.001 TYR B 408 ARG 0.004 0.000 ARG B 58 *********************** 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 : 1.011 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: 0.4094 (OUTLIER) cc_final: 0.1689 (t80) REVERT: B 10 ARG cc_start: 0.3547 (OUTLIER) cc_final: 0.0229 (tpt170) REVERT: B 36 MET cc_start: -0.1552 (OUTLIER) cc_final: -0.3102 (pmt) REVERT: B 94 MET cc_start: 0.1776 (mtt) cc_final: 0.1150 (mtt) REVERT: B 132 THR cc_start: 0.3317 (OUTLIER) cc_final: 0.2757 (p) REVERT: B 155 HIS cc_start: 0.5479 (OUTLIER) cc_final: 0.4541 (m90) REVERT: B 282 LEU cc_start: 0.1109 (OUTLIER) cc_final: 0.0821 (tp) REVERT: B 284 ASN cc_start: 0.1380 (OUTLIER) cc_final: -0.1666 (m-40) REVERT: B 309 ARG cc_start: 0.4448 (OUTLIER) cc_final: 0.0825 (mpt180) REVERT: B 360 MET cc_start: 0.1675 (ptt) cc_final: -0.0008 (mmt) REVERT: B 431 TYR cc_start: 0.6000 (m-80) cc_final: 0.5067 (m-80) REVERT: C 1 MET cc_start: 0.2938 (mmt) cc_final: 0.2472 (mmt) REVERT: C 36 MET cc_start: 0.2189 (OUTLIER) cc_final: 0.1662 (tpt) REVERT: C 82 TYR cc_start: 0.1853 (m-80) cc_final: 0.1179 (m-80) REVERT: C 85 ARG cc_start: 0.4126 (mtm180) cc_final: 0.0183 (ttp-170) REVERT: C 86 ASP cc_start: 0.1740 (OUTLIER) cc_final: 0.1319 (m-30) REVERT: C 155 HIS cc_start: 0.5064 (OUTLIER) cc_final: 0.3721 (m90) REVERT: C 181 TRP cc_start: 0.2101 (OUTLIER) cc_final: 0.1586 (m-10) REVERT: C 205 GLU cc_start: 0.0290 (OUTLIER) cc_final: -0.0017 (tp30) REVERT: C 276 VAL cc_start: 0.0312 (OUTLIER) cc_final: -0.0513 (m) REVERT: C 285 LYS cc_start: 0.4500 (tppt) cc_final: 0.4088 (ttpt) outliers start: 55 outliers final: 39 residues processed: 102 average time/residue: 0.4355 time to fit residues: 58.9649 Evaluate side-chains 103 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 50 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 215 THR 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 282 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 309 ARG 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 146 MET 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 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: 6.9990 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.2631 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 6750 Z= 0.332 Angle : 0.771 6.724 9128 Z= 0.419 Chirality : 0.045 0.161 1026 Planarity : 0.007 0.079 1198 Dihedral : 10.260 57.675 991 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.52 % Favored : 85.14 % Rotamer: Outliers : 8.06 % Allowed : 18.77 % Favored : 73.17 % 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: -3.66 (0.26), residues: 868 helix: -1.66 (0.28), residues: 297 sheet: -3.70 (0.42), residues: 100 loop : -2.69 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 303 HIS 0.006 0.001 HIS B 0 PHE 0.028 0.002 PHE B 165 TYR 0.017 0.002 TYR B 408 ARG 0.006 0.001 ARG B 58 ********************** 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 109 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 54 time to evaluate : 1.015 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 8 TYR cc_start: 0.4208 (OUTLIER) cc_final: 0.2190 (t80) REVERT: B 10 ARG cc_start: 0.3602 (OUTLIER) cc_final: 0.0080 (tpt170) REVERT: B 36 MET cc_start: -0.1663 (OUTLIER) cc_final: -0.3282 (pmt) REVERT: B 58 ARG cc_start: 0.3182 (OUTLIER) cc_final: -0.1399 (mmt-90) REVERT: B 132 THR cc_start: 0.3602 (OUTLIER) cc_final: 0.3064 (p) REVERT: B 155 HIS cc_start: 0.5645 (OUTLIER) cc_final: 0.4860 (m90) REVERT: B 284 ASN cc_start: 0.1672 (OUTLIER) cc_final: -0.1974 (p0) REVERT: B 309 ARG cc_start: 0.4758 (OUTLIER) cc_final: 0.1179 (mpt180) REVERT: B 360 MET cc_start: 0.1787 (ptt) cc_final: -0.0006 (mmt) REVERT: B 431 TYR cc_start: 0.6029 (m-80) cc_final: 0.5170 (m-80) REVERT: C 1 MET cc_start: 0.2853 (mmt) cc_final: 0.2401 (mmt) REVERT: C 82 TYR cc_start: 0.1792 (m-80) cc_final: 0.1189 (m-80) REVERT: C 85 ARG cc_start: 0.4135 (mtm180) cc_final: 0.0318 (ttp-170) REVERT: C 86 ASP cc_start: 0.1528 (OUTLIER) cc_final: 0.1153 (m-30) REVERT: C 155 HIS cc_start: 0.4970 (OUTLIER) cc_final: 0.3630 (m170) REVERT: C 181 TRP cc_start: 0.2197 (OUTLIER) cc_final: 0.1566 (m-10) REVERT: C 205 GLU cc_start: 0.0708 (OUTLIER) cc_final: 0.0211 (tp30) REVERT: C 276 VAL cc_start: 0.0537 (OUTLIER) cc_final: -0.0216 (t) REVERT: C 285 LYS cc_start: 0.4563 (tppt) cc_final: 0.4215 (ttpt) outliers start: 55 outliers final: 40 residues processed: 103 average time/residue: 0.4378 time to fit residues: 59.4118 Evaluate side-chains 107 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 54 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 74 ILE 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 238 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 263 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 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 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 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 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 62 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5398 r_free = 0.5398 target = 0.357274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5395 r_free = 0.5395 target = 0.356868 restraints weight = 26783.586| |-----------------------------------------------------------------------------| r_work (start): 0.5396 rms_B_bonded: 0.09 r_work: 0.5393 rms_B_bonded: 0.12 restraints_weight: 0.5000 r_work: 0.5387 rms_B_bonded: 0.28 restraints_weight: 0.2500 r_work: 0.5337 rms_B_bonded: 2.06 restraints_weight: 0.1250 r_work (final): 0.5337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2577 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6750 Z= 0.179 Angle : 0.609 5.443 9128 Z= 0.328 Chirality : 0.042 0.148 1026 Planarity : 0.005 0.065 1198 Dihedral : 9.358 59.499 991 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.33 % Favored : 90.55 % Rotamer: Outliers : 4.99 % Allowed : 21.26 % Favored : 73.75 % 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: -3.33 (0.26), residues: 868 helix: -1.30 (0.29), residues: 310 sheet: -3.36 (0.46), residues: 98 loop : -2.64 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 300 HIS 0.004 0.001 HIS B 0 PHE 0.022 0.002 PHE B 165 TYR 0.016 0.001 TYR B 408 ARG 0.003 0.001 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3333.41 seconds wall clock time: 60 minutes 6.13 seconds (3606.13 seconds total)