Starting phenix.real_space_refine on Sat Feb 17 11:47:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb8_12257/02_2024/7nb8_12257_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb8_12257/02_2024/7nb8_12257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb8_12257/02_2024/7nb8_12257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb8_12257/02_2024/7nb8_12257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb8_12257/02_2024/7nb8_12257_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb8_12257/02_2024/7nb8_12257_updated.pdb" } resolution = 4.4 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 ------------------------------------------------------------------------------- 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= 0.007 sd= 0.019 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 5906 2.51 5 N 1596 2.21 5 O 1815 1.98 5 H 9185 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18570 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6636 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 6588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "K" Number of atoms: 5280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 5280 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 3, 'TRANS': 319} Chain breaks: 5 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.85, per 1000 atoms: 0.48 Number of scatterers: 18570 At special positions: 0 Unit cell: (98.69, 105.64, 113.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 60 16.00 P 6 15.00 Mg 2 11.99 O 1815 8.00 N 1596 7.00 C 5906 6.00 H 9185 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: 16.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 10 sheets defined 44.8% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 11 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 82 through 85 removed outlier: 3.615A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 128 removed outlier: 5.131A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.516A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.547A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 240 through 243 No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.857A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.657A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.507A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.183A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.501A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 108 through 125 Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.585A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 removed outlier: 4.118A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 236 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.546A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.551A pdb=" N LYS B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 387 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B 390 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 4.481A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.662A pdb=" N GLU B 410 " --> pdb=" O GLU B 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 37 Processing helix chain 'K' and resid 58 through 60 No H-bonds generated for 'chain 'K' and resid 58 through 60' Processing helix chain 'K' and resid 79 through 96 removed outlier: 5.078A pdb=" N TYR K 88 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLN K 89 " --> pdb=" O ASN K 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN K 96 " --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 115 No H-bonds generated for 'chain 'K' and resid 112 through 115' Processing helix chain 'K' and resid 157 through 176 Processing helix chain 'K' and resid 240 through 253 removed outlier: 3.937A pdb=" N LYS K 252 " --> pdb=" O CYS K 248 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS K 253 " --> pdb=" O SER K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 308 No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 314 through 338 removed outlier: 3.607A pdb=" N SER K 326 " --> pdb=" O ASN K 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 344 through 347 Processing helix chain 'K' and resid 350 through 354 Processing helix chain 'K' and resid 356 through 358 No H-bonds generated for 'chain 'K' and resid 356 through 358' Processing helix chain 'K' and resid 375 through 393 removed outlier: 5.387A pdb=" N ASP K 379 " --> pdb=" O LEU K 376 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG K 390 " --> pdb=" O TYR K 387 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.964A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.825A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 51 through 54 Processing sheet with id= E, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.649A pdb=" N ASP B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.848A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 267 through 271 Processing sheet with id= H, first strand: chain 'K' and resid 71 through 73 removed outlier: 8.588A pdb=" N LYS K 23 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR K 365 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE K 25 " --> pdb=" O THR K 365 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE K 367 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ARG K 27 " --> pdb=" O ILE K 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA K 369 " --> pdb=" O ARG K 27 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ARG K 29 " --> pdb=" O ALA K 369 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE K 371 " --> pdb=" O ARG K 29 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN K 99 " --> pdb=" O LYS K 364 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N PHE K 366 " --> pdb=" O ASN K 99 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR K 101 " --> pdb=" O PHE K 366 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL K 368 " --> pdb=" O THR K 101 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE K 103 " --> pdb=" O VAL K 368 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR K 370 " --> pdb=" O PHE K 103 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR K 105 " --> pdb=" O THR K 370 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N SER K 372 " --> pdb=" O TYR K 105 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 45 through 48 Processing sheet with id= J, first strand: chain 'K' and resid 194 through 197 412 hydrogen bonds defined for protein. 999 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: 7.22 Time building geometry restraints manager: 17.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 9156 1.13 - 1.31: 1734 1.31 - 1.49: 4057 1.49 - 1.67: 3708 1.67 - 1.85: 95 Bond restraints: 18750 Sorted by residual: bond pdb=" CB ASP B 67 " pdb=" CG ASP B 67 " ideal model delta sigma weight residual 1.516 1.846 -0.330 2.50e-02 1.60e+03 1.74e+02 bond pdb=" CB ASP A 69 " pdb=" CG ASP A 69 " ideal model delta sigma weight residual 1.516 1.779 -0.263 2.50e-02 1.60e+03 1.10e+02 bond pdb=" NH2 ARG A 243 " pdb="HH22 ARG A 243 " ideal model delta sigma weight residual 0.860 1.053 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" NH1 ARG B 213 " pdb="HH11 ARG B 213 " ideal model delta sigma weight residual 0.860 1.048 -0.188 2.00e-02 2.50e+03 8.86e+01 bond pdb=" NH1 ARG A 156 " pdb="HH12 ARG A 156 " ideal model delta sigma weight residual 0.860 1.047 -0.187 2.00e-02 2.50e+03 8.71e+01 ... (remaining 18745 not shown) Histogram of bond angle deviations from ideal: 93.29 - 102.70: 133 102.70 - 112.11: 20605 112.11 - 121.52: 10477 121.52 - 130.93: 2520 130.93 - 140.34: 52 Bond angle restraints: 33787 Sorted by residual: angle pdb=" N VAL A 260 " pdb=" CA VAL A 260 " pdb=" C VAL A 260 " ideal model delta sigma weight residual 107.56 116.86 -9.30 9.10e-01 1.21e+00 1.04e+02 angle pdb=" CA ASP B 249 " pdb=" CB ASP B 249 " pdb=" CG ASP B 249 " ideal model delta sigma weight residual 112.60 120.22 -7.62 1.00e+00 1.00e+00 5.81e+01 angle pdb=" CA ASP A 205 " pdb=" CB ASP A 205 " pdb=" CG ASP A 205 " ideal model delta sigma weight residual 112.60 119.88 -7.28 1.00e+00 1.00e+00 5.30e+01 angle pdb=" N TYR K 185 " pdb=" CA TYR K 185 " pdb=" C TYR K 185 " ideal model delta sigma weight residual 113.50 101.67 11.83 1.65e+00 3.67e-01 5.14e+01 angle pdb=" N SER K 320 " pdb=" CA SER K 320 " pdb=" C SER K 320 " ideal model delta sigma weight residual 111.28 103.50 7.78 1.09e+00 8.42e-01 5.09e+01 ... (remaining 33782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.42: 8652 33.42 - 66.84: 187 66.84 - 100.26: 16 100.26 - 133.68: 1 133.68 - 167.09: 2 Dihedral angle restraints: 8858 sinusoidal: 4848 harmonic: 4010 Sorted by residual: dihedral pdb=" O3B GTP A 500 " pdb=" O3A GTP A 500 " pdb=" PB GTP A 500 " pdb=" PA GTP A 500 " ideal model delta sinusoidal sigma weight residual 291.08 123.98 167.09 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP A 500 " pdb=" C1' GTP A 500 " pdb=" N9 GTP A 500 " pdb=" O4' GTP A 500 " ideal model delta sinusoidal sigma weight residual 104.59 -45.21 149.80 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" CD2 HIS A 192 " pdb=" CG HIS A 192 " pdb=" ND1 HIS A 192 " pdb=" HD1 HIS A 192 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 8855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 968 0.086 - 0.172: 380 0.172 - 0.258: 80 0.258 - 0.344: 13 0.344 - 0.429: 2 Chirality restraints: 1443 Sorted by residual: chirality pdb=" C3' G2P B 500 " pdb=" C2' G2P B 500 " pdb=" C4' G2P B 500 " pdb=" O3' G2P B 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA ILE K 378 " pdb=" N ILE K 378 " pdb=" C ILE K 378 " pdb=" CB ILE K 378 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PHE K 159 " pdb=" N PHE K 159 " pdb=" C PHE K 159 " pdb=" CB PHE K 159 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1440 not shown) Planarity restraints: 2793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP A 500 " -0.891 2.00e-02 2.50e+03 3.92e-01 4.62e+03 pdb=" C2 GTP A 500 " 0.207 2.00e-02 2.50e+03 pdb=" C4 GTP A 500 " 0.450 2.00e-02 2.50e+03 pdb=" C5 GTP A 500 " 0.075 2.00e-02 2.50e+03 pdb=" C6 GTP A 500 " -0.185 2.00e-02 2.50e+03 pdb=" C8 GTP A 500 " 0.152 2.00e-02 2.50e+03 pdb=" N1 GTP A 500 " -0.435 2.00e-02 2.50e+03 pdb=" N2 GTP A 500 " -0.074 2.00e-02 2.50e+03 pdb=" N3 GTP A 500 " 0.693 2.00e-02 2.50e+03 pdb=" N7 GTP A 500 " 0.160 2.00e-02 2.50e+03 pdb=" N9 GTP A 500 " 0.056 2.00e-02 2.50e+03 pdb=" O6 GTP A 500 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 192 " -0.113 2.00e-02 2.50e+03 1.09e-01 2.69e+02 pdb=" CG HIS A 192 " -0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS A 192 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 HIS A 192 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A 192 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS A 192 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS A 192 " 0.253 2.00e-02 2.50e+03 pdb=" HD2 HIS A 192 " 0.085 2.00e-02 2.50e+03 pdb=" HE1 HIS A 192 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 307 " 0.095 2.00e-02 2.50e+03 1.05e-01 2.50e+02 pdb=" CG HIS B 307 " 0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS B 307 " 0.102 2.00e-02 2.50e+03 pdb=" CD2 HIS B 307 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS B 307 " 0.051 2.00e-02 2.50e+03 pdb=" NE2 HIS B 307 " -0.027 2.00e-02 2.50e+03 pdb=" HD1 HIS B 307 " -0.245 2.00e-02 2.50e+03 pdb=" HD2 HIS B 307 " -0.086 2.00e-02 2.50e+03 pdb=" HE1 HIS B 307 " 0.073 2.00e-02 2.50e+03 ... (remaining 2790 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 370 1.87 - 2.56: 17580 2.56 - 3.24: 60089 3.24 - 3.92: 77370 3.92 - 4.60: 120369 Nonbonded interactions: 275778 Sorted by model distance: nonbonded pdb=" HG1 THR B 166 " pdb=" HG1 THR B 196 " model vdw 1.193 2.100 nonbonded pdb=" HG1 THR B 107 " pdb=" H GLU B 108 " model vdw 1.240 2.100 nonbonded pdb=" H TYR K 185 " pdb=" H ASP K 186 " model vdw 1.281 2.100 nonbonded pdb=" OE1 GLU B 343 " pdb=" H GLU B 343 " model vdw 1.319 1.850 nonbonded pdb=" H ARG B 309 " pdb=" HG1 THR B 372 " model vdw 1.573 2.100 ... (remaining 275773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.020 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: 0.290 Extract box with map and model: 1.320 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 65.650 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.018 0.330 9565 Z= 1.183 Angle : 1.788 15.385 12951 Z= 1.186 Chirality : 0.093 0.429 1443 Planarity : 0.014 0.392 1668 Dihedral : 12.102 167.095 3570 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.85 % Favored : 96.81 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.52 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1159 helix: 0.18 (0.22), residues: 488 sheet: 0.19 (0.39), residues: 189 loop : -0.05 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.007 TRP B 21 HIS 0.012 0.003 HIS A 8 PHE 0.042 0.006 PHE K 103 TYR 0.046 0.009 TYR A 108 ARG 0.015 0.001 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 516 time to evaluate : 1.615 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: 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: 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: 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: 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: 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: 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: A 23 LEU cc_start: 0.8950 (tp) cc_final: 0.8162 (tp) REVERT: A 96 LYS cc_start: 0.7976 (mttt) cc_final: 0.7035 (mtmt) REVERT: A 110 ILE cc_start: 0.8726 (mm) cc_final: 0.8444 (tp) REVERT: A 139 HIS cc_start: 0.7696 (p-80) cc_final: 0.7474 (p90) REVERT: A 189 LEU cc_start: 0.9547 (mt) cc_final: 0.9261 (mt) REVERT: A 235 VAL cc_start: 0.9340 (t) cc_final: 0.8957 (p) REVERT: A 292 THR cc_start: 0.8703 (m) cc_final: 0.8239 (p) REVERT: A 295 CYS cc_start: 0.8700 (m) cc_final: 0.7965 (m) REVERT: A 377 MET cc_start: 0.7876 (ttm) cc_final: 0.6747 (tmm) REVERT: A 417 GLU cc_start: 0.8836 (mt-10) cc_final: 0.7360 (tt0) REVERT: B 150 LEU cc_start: 0.9107 (tp) cc_final: 0.8740 (tt) REVERT: B 267 MET cc_start: 0.7961 (mtt) cc_final: 0.7704 (mmm) REVERT: B 350 LYS cc_start: 0.8757 (tptp) cc_final: 0.8546 (tptp) REVERT: B 366 THR cc_start: 0.7809 (m) cc_final: 0.7083 (p) REVERT: B 377 LEU cc_start: 0.8661 (tp) cc_final: 0.7918 (tp) REVERT: B 407 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7394 (mt-10) outliers start: 1 outliers final: 1 residues processed: 517 average time/residue: 0.6563 time to fit residues: 434.4479 Evaluate side-chains 301 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9565 Z= 0.279 Angle : 0.695 8.826 12951 Z= 0.393 Chirality : 0.046 0.258 1443 Planarity : 0.006 0.062 1668 Dihedral : 11.134 174.266 1324 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.07 % Rotamer: Outliers : 0.10 % Allowed : 1.65 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1159 helix: 0.01 (0.22), residues: 485 sheet: -0.07 (0.38), residues: 210 loop : -0.07 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.005 0.001 HIS B 190 PHE 0.017 0.002 PHE B 242 TYR 0.021 0.002 TYR K 88 ARG 0.007 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 1.699 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: 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: 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: 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: A 23 LEU cc_start: 0.8966 (tp) cc_final: 0.8167 (tp) REVERT: A 80 THR cc_start: 0.8827 (p) cc_final: 0.8415 (t) REVERT: A 96 LYS cc_start: 0.7964 (mttt) cc_final: 0.7347 (mtmt) REVERT: A 110 ILE cc_start: 0.8790 (mm) cc_final: 0.8465 (tp) REVERT: A 139 HIS cc_start: 0.7859 (p-80) cc_final: 0.7626 (p90) REVERT: A 157 LEU cc_start: 0.9428 (mt) cc_final: 0.8740 (tp) REVERT: A 189 LEU cc_start: 0.9615 (mt) cc_final: 0.9364 (mt) REVERT: A 235 VAL cc_start: 0.9137 (t) cc_final: 0.8908 (p) REVERT: A 237 SER cc_start: 0.9163 (m) cc_final: 0.8612 (p) REVERT: A 255 PHE cc_start: 0.8093 (t80) cc_final: 0.7747 (t80) REVERT: A 313 MET cc_start: 0.7966 (mmm) cc_final: 0.7385 (mmm) REVERT: A 377 MET cc_start: 0.7173 (ttm) cc_final: 0.6200 (tmm) REVERT: B 69 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8156 (mt-10) REVERT: B 215 LEU cc_start: 0.8566 (mt) cc_final: 0.8302 (mt) REVERT: K 198 ASN cc_start: 0.7035 (t0) cc_final: 0.6793 (t0) REVERT: K 227 LEU cc_start: 0.7744 (tp) cc_final: 0.7465 (tp) REVERT: K 294 LEU cc_start: 0.7716 (tp) cc_final: 0.7394 (tp) REVERT: K 295 ASN cc_start: 0.6873 (m-40) cc_final: 0.6460 (m110) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.5474 time to fit residues: 241.1197 Evaluate side-chains 253 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 104 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 139 HIS A 309 HIS A 380 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN ** K 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9565 Z= 0.223 Angle : 0.589 5.586 12951 Z= 0.330 Chirality : 0.042 0.208 1443 Planarity : 0.005 0.050 1668 Dihedral : 10.694 179.716 1324 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1159 helix: 0.13 (0.23), residues: 473 sheet: -0.15 (0.39), residues: 216 loop : 0.05 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 346 HIS 0.007 0.001 HIS A 197 PHE 0.017 0.002 PHE A 149 TYR 0.017 0.001 TYR K 197 ARG 0.004 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.703 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7911 (mt) cc_final: 0.7631 (mp) REVERT: A 80 THR cc_start: 0.8822 (p) cc_final: 0.8510 (t) REVERT: A 96 LYS cc_start: 0.7912 (mttt) cc_final: 0.7522 (mtmt) REVERT: A 110 ILE cc_start: 0.8946 (mm) cc_final: 0.8517 (tp) REVERT: A 139 HIS cc_start: 0.7966 (p90) cc_final: 0.7503 (p90) REVERT: A 235 VAL cc_start: 0.9124 (t) cc_final: 0.8815 (p) REVERT: A 237 SER cc_start: 0.8977 (m) cc_final: 0.8517 (p) REVERT: A 255 PHE cc_start: 0.8233 (t80) cc_final: 0.7844 (t80) REVERT: A 420 GLU cc_start: 0.7362 (pm20) cc_final: 0.7075 (mp0) REVERT: B 300 MET cc_start: 0.8748 (mtm) cc_final: 0.8526 (mtm) REVERT: B 350 LYS cc_start: 0.8749 (tptp) cc_final: 0.8473 (tptp) REVERT: K 189 ILE cc_start: 0.7970 (mt) cc_final: 0.7721 (mt) REVERT: K 295 ASN cc_start: 0.6595 (m-40) cc_final: 0.6065 (m110) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.5761 time to fit residues: 225.4565 Evaluate side-chains 228 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9565 Z= 0.241 Angle : 0.574 5.562 12951 Z= 0.319 Chirality : 0.042 0.193 1443 Planarity : 0.005 0.049 1668 Dihedral : 10.361 175.478 1324 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1159 helix: 0.07 (0.23), residues: 480 sheet: -0.24 (0.38), residues: 212 loop : 0.02 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 21 HIS 0.006 0.001 HIS B 37 PHE 0.013 0.002 PHE K 366 TYR 0.023 0.002 TYR B 159 ARG 0.005 0.001 ARG K 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.691 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: 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: 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: A 70 LEU cc_start: 0.7931 (mt) cc_final: 0.7632 (mp) REVERT: A 76 ASP cc_start: 0.8289 (m-30) cc_final: 0.8058 (m-30) REVERT: A 80 THR cc_start: 0.8793 (p) cc_final: 0.8547 (t) REVERT: A 110 ILE cc_start: 0.9077 (mm) cc_final: 0.8629 (tp) REVERT: A 139 HIS cc_start: 0.8382 (p90) cc_final: 0.7928 (p90) REVERT: A 182 VAL cc_start: 0.8277 (m) cc_final: 0.8065 (m) REVERT: A 209 ILE cc_start: 0.9436 (mm) cc_final: 0.9054 (mm) REVERT: A 235 VAL cc_start: 0.9099 (t) cc_final: 0.8836 (p) REVERT: A 237 SER cc_start: 0.9073 (m) cc_final: 0.8573 (p) REVERT: A 262 TYR cc_start: 0.6814 (m-10) cc_final: 0.5217 (m-80) REVERT: A 295 CYS cc_start: 0.8745 (m) cc_final: 0.8286 (m) REVERT: A 302 MET cc_start: 0.8772 (mtp) cc_final: 0.8528 (mtt) REVERT: A 313 MET cc_start: 0.7965 (mmm) cc_final: 0.7740 (mmm) REVERT: A 352 LYS cc_start: 0.3059 (mmtt) cc_final: 0.2518 (mmtm) REVERT: A 417 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7978 (mt-10) REVERT: A 420 GLU cc_start: 0.7419 (pm20) cc_final: 0.7163 (mp0) REVERT: B 19 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8874 (mmmm) REVERT: K 52 VAL cc_start: 0.7352 (t) cc_final: 0.6469 (t) REVERT: K 227 LEU cc_start: 0.7844 (tp) cc_final: 0.7637 (tp) REVERT: K 295 ASN cc_start: 0.6605 (m-40) cc_final: 0.6173 (m110) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.5272 time to fit residues: 194.2778 Evaluate side-chains 227 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN B 105 HIS ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.7537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9565 Z= 0.187 Angle : 0.532 6.575 12951 Z= 0.293 Chirality : 0.041 0.188 1443 Planarity : 0.004 0.044 1668 Dihedral : 10.040 175.604 1324 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1159 helix: 0.21 (0.23), residues: 490 sheet: -0.38 (0.38), residues: 219 loop : 0.00 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 388 HIS 0.008 0.001 HIS A 28 PHE 0.021 0.001 PHE K 69 TYR 0.030 0.002 TYR A 432 ARG 0.007 0.000 ARG K 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.608 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7884 (mt) cc_final: 0.7600 (mp) REVERT: A 80 THR cc_start: 0.8728 (p) cc_final: 0.8519 (t) REVERT: A 96 LYS cc_start: 0.8048 (mttt) cc_final: 0.7634 (mtmt) REVERT: A 110 ILE cc_start: 0.9058 (mm) cc_final: 0.8611 (tp) REVERT: A 139 HIS cc_start: 0.8262 (p90) cc_final: 0.7553 (p90) REVERT: A 209 ILE cc_start: 0.9397 (mm) cc_final: 0.8983 (mm) REVERT: A 235 VAL cc_start: 0.9111 (t) cc_final: 0.8807 (p) REVERT: A 237 SER cc_start: 0.9077 (m) cc_final: 0.8606 (p) REVERT: A 295 CYS cc_start: 0.8566 (m) cc_final: 0.8247 (m) REVERT: A 302 MET cc_start: 0.8741 (mtp) cc_final: 0.8469 (mtt) REVERT: A 313 MET cc_start: 0.8053 (mmm) cc_final: 0.7851 (mmm) REVERT: A 352 LYS cc_start: 0.3025 (mmtt) cc_final: 0.2517 (mmtm) REVERT: B 19 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8822 (mmmm) REVERT: K 227 LEU cc_start: 0.7682 (tp) cc_final: 0.7463 (tp) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.5219 time to fit residues: 191.1780 Evaluate side-chains 216 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.8006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9565 Z= 0.301 Angle : 0.587 5.536 12951 Z= 0.328 Chirality : 0.041 0.190 1443 Planarity : 0.005 0.046 1668 Dihedral : 9.841 170.028 1324 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1159 helix: -0.08 (0.22), residues: 491 sheet: -0.52 (0.37), residues: 221 loop : -0.31 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 346 HIS 0.007 0.002 HIS B 37 PHE 0.019 0.002 PHE K 69 TYR 0.023 0.002 TYR K 261 ARG 0.003 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.688 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: 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: 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: symmetry clash REVERT: A 80 THR cc_start: 0.8785 (p) cc_final: 0.8584 (t) REVERT: A 110 ILE cc_start: 0.9171 (mm) cc_final: 0.8779 (tp) REVERT: A 129 CYS cc_start: 0.7597 (p) cc_final: 0.7374 (p) REVERT: A 139 HIS cc_start: 0.8714 (p90) cc_final: 0.8418 (p-80) REVERT: A 209 ILE cc_start: 0.9391 (mm) cc_final: 0.9006 (mm) REVERT: A 235 VAL cc_start: 0.9135 (t) cc_final: 0.8822 (p) REVERT: A 237 SER cc_start: 0.9145 (m) cc_final: 0.8666 (p) REVERT: A 295 CYS cc_start: 0.8647 (m) cc_final: 0.8329 (m) REVERT: A 302 MET cc_start: 0.8801 (mtp) cc_final: 0.8518 (mtt) REVERT: A 313 MET cc_start: 0.8149 (mmm) cc_final: 0.7933 (mmm) REVERT: A 352 LYS cc_start: 0.3436 (mmtt) cc_final: 0.2876 (mmtm) REVERT: B 19 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8933 (mmmm) REVERT: B 311 LEU cc_start: 0.9241 (tp) cc_final: 0.8900 (tt) REVERT: K 189 ILE cc_start: 0.7867 (mt) cc_final: 0.7663 (mt) REVERT: K 227 LEU cc_start: 0.7710 (tp) cc_final: 0.7423 (tp) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.5237 time to fit residues: 183.0963 Evaluate side-chains 209 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9565 Z= 0.241 Angle : 0.545 5.465 12951 Z= 0.308 Chirality : 0.041 0.193 1443 Planarity : 0.004 0.041 1668 Dihedral : 9.654 167.645 1324 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1159 helix: 0.06 (0.23), residues: 489 sheet: -0.60 (0.36), residues: 221 loop : -0.19 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 21 HIS 0.016 0.002 HIS B 6 PHE 0.016 0.002 PHE A 149 TYR 0.018 0.002 TYR A 432 ARG 0.003 0.000 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.650 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: 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: 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: A 110 ILE cc_start: 0.9120 (mm) cc_final: 0.8775 (tp) REVERT: A 129 CYS cc_start: 0.7550 (p) cc_final: 0.7327 (p) REVERT: A 209 ILE cc_start: 0.9388 (mm) cc_final: 0.8939 (mm) REVERT: A 237 SER cc_start: 0.9177 (m) cc_final: 0.8693 (p) REVERT: A 295 CYS cc_start: 0.8644 (m) cc_final: 0.8314 (m) REVERT: A 302 MET cc_start: 0.8828 (mtp) cc_final: 0.8530 (mtt) REVERT: A 313 MET cc_start: 0.8163 (mmm) cc_final: 0.7880 (mmm) REVERT: A 352 LYS cc_start: 0.3224 (mmtt) cc_final: 0.2554 (mmtm) REVERT: A 417 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8188 (mt-10) REVERT: B 19 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8857 (mmmm) REVERT: K 189 ILE cc_start: 0.7809 (mt) cc_final: 0.7523 (mt) REVERT: K 227 LEU cc_start: 0.7719 (tp) cc_final: 0.7447 (tp) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.5234 time to fit residues: 179.6879 Evaluate side-chains 211 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.8491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9565 Z= 0.235 Angle : 0.547 5.534 12951 Z= 0.308 Chirality : 0.041 0.195 1443 Planarity : 0.005 0.041 1668 Dihedral : 9.401 164.578 1324 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1159 helix: -0.06 (0.23), residues: 491 sheet: -0.60 (0.36), residues: 225 loop : -0.26 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 21 HIS 0.006 0.001 HIS B 37 PHE 0.012 0.001 PHE K 187 TYR 0.013 0.002 TYR K 197 ARG 0.006 0.001 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.024 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: 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: 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: A 96 LYS cc_start: 0.8202 (mttt) cc_final: 0.7847 (mtmt) REVERT: A 110 ILE cc_start: 0.9117 (mm) cc_final: 0.8721 (tp) REVERT: A 209 ILE cc_start: 0.9384 (mm) cc_final: 0.9151 (mm) REVERT: A 237 SER cc_start: 0.9202 (m) cc_final: 0.8686 (p) REVERT: A 295 CYS cc_start: 0.8773 (m) cc_final: 0.8465 (m) REVERT: A 302 MET cc_start: 0.8824 (mtp) cc_final: 0.8563 (mtt) REVERT: A 313 MET cc_start: 0.8182 (mmm) cc_final: 0.7913 (mmm) REVERT: A 417 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8207 (mt-10) REVERT: B 7 ILE cc_start: 0.9268 (mm) cc_final: 0.9062 (mm) REVERT: B 19 LYS cc_start: 0.9247 (mmmt) cc_final: 0.8923 (mmmm) REVERT: B 215 LEU cc_start: 0.9002 (mt) cc_final: 0.8787 (mt) REVERT: K 50 ASN cc_start: 0.6025 (t0) cc_final: 0.5760 (t0) REVERT: K 189 ILE cc_start: 0.7772 (mt) cc_final: 0.7510 (mt) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.5730 time to fit residues: 192.0807 Evaluate side-chains 204 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 overall best weight: 5.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN K 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.8665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9565 Z= 0.187 Angle : 0.514 5.513 12951 Z= 0.287 Chirality : 0.041 0.192 1443 Planarity : 0.004 0.041 1668 Dihedral : 8.993 157.571 1324 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1159 helix: 0.15 (0.23), residues: 494 sheet: -0.46 (0.37), residues: 218 loop : -0.13 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 21 HIS 0.010 0.001 HIS A 28 PHE 0.015 0.001 PHE A 255 TYR 0.013 0.001 TYR K 197 ARG 0.002 0.000 ARG K 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.598 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8169 (mttt) cc_final: 0.7569 (mtmt) REVERT: A 110 ILE cc_start: 0.9085 (mm) cc_final: 0.8831 (tp) REVERT: A 209 ILE cc_start: 0.9381 (mm) cc_final: 0.9047 (mm) REVERT: A 237 SER cc_start: 0.9195 (m) cc_final: 0.8673 (p) REVERT: A 295 CYS cc_start: 0.8821 (m) cc_final: 0.8501 (m) REVERT: A 302 MET cc_start: 0.8812 (mtp) cc_final: 0.8548 (mtt) REVERT: A 313 MET cc_start: 0.8040 (mmm) cc_final: 0.7713 (mmm) REVERT: A 352 LYS cc_start: 0.4007 (mptt) cc_final: 0.3308 (mmtm) REVERT: A 417 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8188 (mt-10) REVERT: B 116 VAL cc_start: 0.9142 (t) cc_final: 0.8896 (p) REVERT: B 215 LEU cc_start: 0.9017 (mt) cc_final: 0.8810 (mt) REVERT: B 266 PHE cc_start: 0.8381 (m-80) cc_final: 0.8130 (m-80) REVERT: K 50 ASN cc_start: 0.6096 (t0) cc_final: 0.5874 (t0) REVERT: K 189 ILE cc_start: 0.7788 (mt) cc_final: 0.7515 (mt) REVERT: K 204 LEU cc_start: 0.7178 (tp) cc_final: 0.6968 (tp) REVERT: K 246 ILE cc_start: 0.8450 (mt) cc_final: 0.7880 (tp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.5265 time to fit residues: 173.1592 Evaluate side-chains 203 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 30.0000 chunk 73 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 317 GLN K 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.8796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9565 Z= 0.221 Angle : 0.532 9.068 12951 Z= 0.298 Chirality : 0.040 0.191 1443 Planarity : 0.004 0.042 1668 Dihedral : 8.790 153.291 1324 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1159 helix: 0.06 (0.23), residues: 499 sheet: -0.55 (0.36), residues: 226 loop : -0.12 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 388 HIS 0.010 0.001 HIS A 28 PHE 0.012 0.002 PHE B 20 TYR 0.018 0.002 TYR A 210 ARG 0.003 0.000 ARG A 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.422 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: 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: 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: A 96 LYS cc_start: 0.8060 (mttt) cc_final: 0.7697 (mtmt) REVERT: A 110 ILE cc_start: 0.9109 (mm) cc_final: 0.8802 (tp) REVERT: A 129 CYS cc_start: 0.7588 (p) cc_final: 0.7334 (p) REVERT: A 209 ILE cc_start: 0.9396 (mm) cc_final: 0.9069 (mm) REVERT: A 237 SER cc_start: 0.9206 (m) cc_final: 0.8803 (p) REVERT: A 302 MET cc_start: 0.8818 (mtp) cc_final: 0.8500 (mtt) REVERT: A 315 CYS cc_start: 0.8585 (t) cc_final: 0.8330 (t) REVERT: A 352 LYS cc_start: 0.3828 (mptt) cc_final: 0.3347 (mmtm) REVERT: A 376 CYS cc_start: 0.8224 (t) cc_final: 0.7913 (t) REVERT: A 417 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8101 (mt-10) REVERT: K 50 ASN cc_start: 0.6205 (t0) cc_final: 0.5976 (t0) REVERT: K 189 ILE cc_start: 0.7800 (mt) cc_final: 0.7540 (mt) REVERT: K 246 ILE cc_start: 0.8487 (mt) cc_final: 0.7930 (tp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.5158 time to fit residues: 170.7163 Evaluate side-chains 203 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 25 optimal weight: 0.0010 chunk 92 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN K 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.069881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058250 restraints weight = 106045.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.061389 restraints weight = 46051.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.063382 restraints weight = 24446.524| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.8964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9565 Z= 0.192 Angle : 0.528 6.471 12951 Z= 0.294 Chirality : 0.041 0.190 1443 Planarity : 0.004 0.042 1668 Dihedral : 8.495 146.973 1324 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1159 helix: 0.09 (0.23), residues: 497 sheet: -0.48 (0.36), residues: 226 loop : -0.09 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 346 HIS 0.009 0.001 HIS A 28 PHE 0.013 0.001 PHE B 20 TYR 0.016 0.001 TYR A 210 ARG 0.007 0.000 ARG B 276 =============================================================================== Job complete usr+sys time: 4844.88 seconds wall clock time: 86 minutes 56.86 seconds (5216.86 seconds total)