Starting phenix.real_space_refine on Tue Feb 13 18:09:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/02_2024/7ezk_31388_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/02_2024/7ezk_31388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/02_2024/7ezk_31388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/02_2024/7ezk_31388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/02_2024/7ezk_31388_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/02_2024/7ezk_31388_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 4584 2.51 5 N 1242 2.21 5 O 1313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7196 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1871 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2298 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 388 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.17, per 1000 atoms: 0.58 Number of scatterers: 7196 At special positions: 0 Unit cell: (102.41, 113.905, 101.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1313 8.00 N 1242 7.00 C 4584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " distance=2.04 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: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 9 sheets defined 44.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.726A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.955A pdb=" N ILE A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.974A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 299 through 318 Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.223A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 5.314A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.516A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 68 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 75 through 104 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 144 Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.279A pdb=" N ARG D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 151' Processing helix chain 'D' and resid 155 through 172 Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'D' and resid 219 through 245 Processing helix chain 'D' and resid 302 through 338 Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 350 through 370 removed outlier: 4.281A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 375 through 381 removed outlier: 4.503A pdb=" N GLY D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 23 removed outlier: 3.669A pdb=" N LYS G 20 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 45 Processing sheet with id= A, first strand: chain 'A' and resid 326 through 330 removed outlier: 7.175A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.870A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.012A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.832A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.855A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.369A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.815A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 180 through 186 371 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1832 1.33 - 1.46: 2104 1.46 - 1.60: 3323 1.60 - 1.73: 1 1.73 - 1.86: 84 Bond restraints: 7344 Sorted by residual: bond pdb=" O3 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.458 1.630 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.567 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" O2 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.461 1.411 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" CZ ARG A 347 " pdb=" NH2 ARG A 347 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.21e+00 bond pdb=" CZ ARG A 31 " pdb=" NH1 ARG A 31 " ideal model delta sigma weight residual 1.323 1.354 -0.031 1.40e-02 5.10e+03 4.85e+00 ... (remaining 7339 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.88: 118 104.88 - 112.40: 3568 112.40 - 119.92: 2917 119.92 - 127.45: 3278 127.45 - 134.97: 81 Bond angle restraints: 9962 Sorted by residual: angle pdb=" O2 TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 115.38 103.35 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" OH TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 100.21 110.88 -10.67 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N ARG D 310 " pdb=" CA ARG D 310 " pdb=" C ARG D 310 " ideal model delta sigma weight residual 111.36 107.77 3.59 1.09e+00 8.42e-01 1.08e+01 angle pdb=" CZ TYS P 2 " pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 116.88 126.28 -9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" NE ARG B 48 " pdb=" CZ ARG B 48 " pdb=" NH1 ARG B 48 " ideal model delta sigma weight residual 121.50 118.68 2.82 1.00e+00 1.00e+00 7.93e+00 ... (remaining 9957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4031 17.82 - 35.64: 282 35.64 - 53.46: 41 53.46 - 71.28: 13 71.28 - 89.10: 7 Dihedral angle restraints: 4374 sinusoidal: 1681 harmonic: 2693 Sorted by residual: dihedral pdb=" CA ASP A 217 " pdb=" C ASP A 217 " pdb=" N VAL A 218 " pdb=" CA VAL A 218 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR B 289 " pdb=" C TYR B 289 " pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 4371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 698 0.053 - 0.105: 351 0.105 - 0.157: 81 0.157 - 0.210: 8 0.210 - 0.262: 4 Chirality restraints: 1142 Sorted by residual: chirality pdb=" CG LEU D 214 " pdb=" CB LEU D 214 " pdb=" CD1 LEU D 214 " pdb=" CD2 LEU D 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL D 151 " pdb=" CA VAL D 151 " pdb=" CG1 VAL D 151 " pdb=" CG2 VAL D 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1139 not shown) Planarity restraints: 1261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 300 " 0.064 9.50e-02 1.11e+02 4.95e-02 2.07e+01 pdb=" NE ARG A 300 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 300 " 0.077 2.00e-02 2.50e+03 pdb=" NH1 ARG A 300 " -0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 300 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 367 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C PRO D 367 " -0.066 2.00e-02 2.50e+03 pdb=" O PRO D 367 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE D 368 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 214 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU D 214 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU D 214 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU D 215 " -0.022 2.00e-02 2.50e+03 ... (remaining 1258 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 696 2.74 - 3.28: 7532 3.28 - 3.82: 12140 3.82 - 4.36: 15027 4.36 - 4.90: 25332 Nonbonded interactions: 60727 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.206 2.440 nonbonded pdb=" OD1 ASN D 98 " pdb=" OH TYR D 360 " model vdw 2.286 2.440 nonbonded pdb=" NZ LYS D 115 " pdb=" O PRO D 177 " model vdw 2.308 2.520 nonbonded pdb=" NH2 ARG A 205 " pdb=" OE1 GLU A 207 " model vdw 2.312 2.520 nonbonded pdb=" NH1 ARG D 197 " pdb=" O1 TYS P 2 " model vdw 2.337 2.520 ... (remaining 60722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 0.010 Extract box with map and model: 1.630 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.160 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.011 0.172 7344 Z= 0.684 Angle : 1.037 12.028 9962 Z= 0.616 Chirality : 0.061 0.262 1142 Planarity : 0.010 0.082 1261 Dihedral : 13.268 89.095 2619 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.26 % Allowed : 2.34 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.27), residues: 905 helix: -0.92 (0.22), residues: 399 sheet: 0.04 (0.38), residues: 191 loop : -0.47 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP B 99 HIS 0.020 0.007 HIS A 354 PHE 0.033 0.006 PHE G 61 TYR 0.028 0.008 TYR D 229 ARG 0.078 0.010 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 0.830 Fit side-chains REVERT: A 20 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6164 (mt-10) REVERT: A 216 ASN cc_start: 0.8316 (t0) cc_final: 0.8111 (t0) REVERT: A 223 PHE cc_start: 0.8172 (t80) cc_final: 0.7865 (t80) REVERT: A 276 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6866 (mt-10) REVERT: A 348 ASP cc_start: 0.7331 (t70) cc_final: 0.6992 (t0) REVERT: B 59 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: B 76 ASP cc_start: 0.6661 (t70) cc_final: 0.6347 (t0) REVERT: B 145 TYR cc_start: 0.8301 (p90) cc_final: 0.7667 (p90) REVERT: B 147 SER cc_start: 0.8402 (t) cc_final: 0.8053 (p) REVERT: B 149 CYS cc_start: 0.7155 (p) cc_final: 0.6674 (p) REVERT: B 150 ARG cc_start: 0.8148 (mmt-90) cc_final: 0.7427 (mmt-90) REVERT: B 188 MET cc_start: 0.7168 (tpt) cc_final: 0.6900 (mmm) REVERT: B 189 SER cc_start: 0.8346 (p) cc_final: 0.8026 (t) REVERT: B 191 SER cc_start: 0.8118 (m) cc_final: 0.7915 (p) REVERT: B 201 SER cc_start: 0.8254 (m) cc_final: 0.7588 (p) REVERT: B 273 ILE cc_start: 0.7793 (mt) cc_final: 0.7363 (mt) REVERT: B 277 SER cc_start: 0.8177 (t) cc_final: 0.7701 (m) REVERT: B 295 ASN cc_start: 0.7992 (m-40) cc_final: 0.7720 (m110) REVERT: B 325 MET cc_start: 0.6838 (tpp) cc_final: 0.6452 (tpp) REVERT: B 333 ASP cc_start: 0.6664 (m-30) cc_final: 0.6419 (m-30) REVERT: D 56 VAL cc_start: 0.6996 (t) cc_final: 0.6674 (m) REVERT: D 86 SER cc_start: 0.8548 (t) cc_final: 0.8144 (p) REVERT: D 117 THR cc_start: 0.7240 (m) cc_final: 0.6852 (p) REVERT: D 382 MET cc_start: 0.5512 (mpp) cc_final: 0.5130 (mpp) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.1974 time to fit residues: 58.6042 Evaluate side-chains 196 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 268 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7344 Z= 0.225 Angle : 0.571 5.648 9962 Z= 0.301 Chirality : 0.043 0.147 1142 Planarity : 0.004 0.059 1261 Dihedral : 5.721 49.813 998 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.34 % Allowed : 10.66 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 905 helix: 1.13 (0.26), residues: 395 sheet: -0.15 (0.36), residues: 188 loop : 0.34 (0.39), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 324 PHE 0.014 0.002 PHE A 189 TYR 0.013 0.002 TYR B 289 ARG 0.005 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 224 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7623 (mm) cc_final: 0.7219 (mt) REVERT: A 20 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6185 (mt-10) REVERT: A 27 LYS cc_start: 0.8036 (tttt) cc_final: 0.7713 (tttp) REVERT: A 216 ASN cc_start: 0.8157 (t0) cc_final: 0.7912 (t0) REVERT: A 223 PHE cc_start: 0.8248 (t80) cc_final: 0.8022 (t80) REVERT: A 237 LEU cc_start: 0.8022 (tp) cc_final: 0.7776 (mt) REVERT: A 239 ASP cc_start: 0.6899 (m-30) cc_final: 0.6584 (t0) REVERT: A 276 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6838 (mt-10) REVERT: A 359 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6250 (mt-10) REVERT: B 59 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: B 68 ARG cc_start: 0.7491 (ttt90) cc_final: 0.7227 (ttt90) REVERT: B 145 TYR cc_start: 0.8351 (p90) cc_final: 0.7441 (p90) REVERT: B 147 SER cc_start: 0.8177 (t) cc_final: 0.7914 (p) REVERT: B 149 CYS cc_start: 0.7270 (p) cc_final: 0.6925 (p) REVERT: B 150 ARG cc_start: 0.8393 (mmt-90) cc_final: 0.7790 (mmt-90) REVERT: B 163 ASP cc_start: 0.7156 (p0) cc_final: 0.6885 (p0) REVERT: B 181 THR cc_start: 0.8096 (p) cc_final: 0.7694 (m) REVERT: B 189 SER cc_start: 0.8341 (p) cc_final: 0.8000 (t) REVERT: B 191 SER cc_start: 0.8016 (m) cc_final: 0.7800 (p) REVERT: B 201 SER cc_start: 0.8171 (m) cc_final: 0.7737 (p) REVERT: B 214 ARG cc_start: 0.7083 (mpt90) cc_final: 0.6567 (mpt180) REVERT: B 219 ARG cc_start: 0.6882 (mmt180) cc_final: 0.6582 (mmt180) REVERT: B 253 PHE cc_start: 0.8055 (m-80) cc_final: 0.7803 (m-80) REVERT: B 254 ASP cc_start: 0.6474 (t70) cc_final: 0.6201 (t0) REVERT: B 304 ARG cc_start: 0.7555 (ttm170) cc_final: 0.7328 (ttm170) REVERT: B 316 SER cc_start: 0.7688 (t) cc_final: 0.7439 (p) REVERT: B 318 LEU cc_start: 0.7823 (tp) cc_final: 0.7615 (tt) REVERT: B 325 MET cc_start: 0.6967 (tpp) cc_final: 0.6686 (tpp) REVERT: B 333 ASP cc_start: 0.6583 (m-30) cc_final: 0.6293 (m-30) REVERT: D 56 VAL cc_start: 0.6870 (t) cc_final: 0.6646 (m) REVERT: D 80 LEU cc_start: 0.7517 (mt) cc_final: 0.7205 (mp) REVERT: D 86 SER cc_start: 0.8662 (t) cc_final: 0.8402 (p) REVERT: D 104 LEU cc_start: 0.7912 (mt) cc_final: 0.7678 (mt) REVERT: D 118 THR cc_start: 0.8537 (t) cc_final: 0.8090 (p) REVERT: D 121 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6925 (mtt) REVERT: D 136 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7427 (p) REVERT: D 173 MET cc_start: 0.7361 (mmp) cc_final: 0.7074 (mmt) REVERT: D 195 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6109 (mtm) outliers start: 18 outliers final: 10 residues processed: 228 average time/residue: 0.2353 time to fit residues: 69.5175 Evaluate side-chains 227 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7344 Z= 0.219 Angle : 0.522 6.167 9962 Z= 0.274 Chirality : 0.042 0.136 1142 Planarity : 0.004 0.056 1261 Dihedral : 5.356 50.073 998 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.25 % Allowed : 12.87 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 905 helix: 1.57 (0.27), residues: 384 sheet: -0.41 (0.35), residues: 200 loop : 0.49 (0.40), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 324 PHE 0.015 0.001 PHE A 189 TYR 0.011 0.001 TYR D 176 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6215 (mt-10) REVERT: A 186 GLU cc_start: 0.6669 (tt0) cc_final: 0.6428 (tt0) REVERT: A 216 ASN cc_start: 0.8091 (t0) cc_final: 0.7873 (t0) REVERT: A 239 ASP cc_start: 0.6971 (m-30) cc_final: 0.6753 (m-30) REVERT: A 242 SER cc_start: 0.7959 (p) cc_final: 0.7652 (p) REVERT: A 267 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8133 (mttp) REVERT: A 276 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6826 (mt-10) REVERT: A 311 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5316 (mm-30) REVERT: A 314 ARG cc_start: 0.7336 (ttm170) cc_final: 0.6860 (ttm170) REVERT: B 48 ARG cc_start: 0.8215 (mmt-90) cc_final: 0.8011 (mmt180) REVERT: B 59 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: B 68 ARG cc_start: 0.7612 (ttt90) cc_final: 0.7268 (ttt90) REVERT: B 119 ASN cc_start: 0.8320 (m-40) cc_final: 0.7970 (m-40) REVERT: B 147 SER cc_start: 0.8149 (t) cc_final: 0.7935 (p) REVERT: B 149 CYS cc_start: 0.7236 (p) cc_final: 0.6840 (p) REVERT: B 150 ARG cc_start: 0.8378 (mmt-90) cc_final: 0.7768 (mmt-90) REVERT: B 189 SER cc_start: 0.8278 (p) cc_final: 0.8003 (p) REVERT: B 195 ASP cc_start: 0.7937 (p0) cc_final: 0.7700 (p0) REVERT: B 196 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7678 (m) REVERT: B 201 SER cc_start: 0.8231 (m) cc_final: 0.7897 (p) REVERT: B 214 ARG cc_start: 0.7235 (mpt90) cc_final: 0.6664 (mpt180) REVERT: B 219 ARG cc_start: 0.6957 (mmt180) cc_final: 0.6521 (mmt-90) REVERT: B 233 CYS cc_start: 0.7475 (t) cc_final: 0.7269 (t) REVERT: B 253 PHE cc_start: 0.8120 (m-80) cc_final: 0.7909 (m-80) REVERT: B 304 ARG cc_start: 0.7655 (ttm170) cc_final: 0.7346 (ttm170) REVERT: B 322 ASP cc_start: 0.5964 (t0) cc_final: 0.5705 (t0) REVERT: B 325 MET cc_start: 0.6978 (tpp) cc_final: 0.6632 (tpp) REVERT: D 56 VAL cc_start: 0.7059 (t) cc_final: 0.6811 (m) REVERT: D 86 SER cc_start: 0.8632 (t) cc_final: 0.8422 (p) REVERT: D 104 LEU cc_start: 0.7935 (mt) cc_final: 0.7685 (mt) REVERT: D 121 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7036 (mtm) REVERT: D 136 SER cc_start: 0.7987 (t) cc_final: 0.7413 (p) REVERT: D 382 MET cc_start: 0.5783 (mpp) cc_final: 0.5366 (mpp) outliers start: 25 outliers final: 15 residues processed: 229 average time/residue: 0.2309 time to fit residues: 67.1587 Evaluate side-chains 233 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 268 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7344 Z= 0.270 Angle : 0.548 6.922 9962 Z= 0.283 Chirality : 0.044 0.137 1142 Planarity : 0.004 0.058 1261 Dihedral : 5.251 50.043 998 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.29 % Allowed : 13.78 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.29), residues: 905 helix: 1.63 (0.27), residues: 384 sheet: -0.44 (0.35), residues: 193 loop : 0.36 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 324 PHE 0.018 0.002 PHE A 189 TYR 0.014 0.002 TYR D 176 ARG 0.006 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7423 (mmtt) cc_final: 0.6971 (mmtt) REVERT: A 20 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6287 (mt-10) REVERT: A 186 GLU cc_start: 0.6736 (tt0) cc_final: 0.6493 (tt0) REVERT: A 276 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6816 (mt-10) REVERT: A 311 GLU cc_start: 0.6233 (mm-30) cc_final: 0.5984 (mm-30) REVERT: A 335 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: B 59 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: B 83 ASP cc_start: 0.7591 (t0) cc_final: 0.7273 (t70) REVERT: B 101 MET cc_start: 0.7864 (mtp) cc_final: 0.7590 (mtp) REVERT: B 119 ASN cc_start: 0.8463 (m-40) cc_final: 0.8164 (m-40) REVERT: B 139 LEU cc_start: 0.8490 (mt) cc_final: 0.8260 (mt) REVERT: B 145 TYR cc_start: 0.8267 (p90) cc_final: 0.7366 (p90) REVERT: B 147 SER cc_start: 0.8190 (t) cc_final: 0.7890 (p) REVERT: B 150 ARG cc_start: 0.8375 (mmt-90) cc_final: 0.7909 (mmt-90) REVERT: B 189 SER cc_start: 0.8168 (p) cc_final: 0.7923 (p) REVERT: B 195 ASP cc_start: 0.7967 (p0) cc_final: 0.7756 (p0) REVERT: B 196 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7653 (m) REVERT: B 201 SER cc_start: 0.8271 (m) cc_final: 0.7988 (p) REVERT: B 214 ARG cc_start: 0.7260 (mpt90) cc_final: 0.6646 (mpt180) REVERT: B 219 ARG cc_start: 0.6989 (mmt180) cc_final: 0.6526 (mmt-90) REVERT: B 233 CYS cc_start: 0.7766 (t) cc_final: 0.7356 (t) REVERT: B 277 SER cc_start: 0.8044 (t) cc_final: 0.7487 (m) REVERT: B 304 ARG cc_start: 0.7762 (ttm170) cc_final: 0.7418 (ttm170) REVERT: B 312 ASP cc_start: 0.6486 (t0) cc_final: 0.5839 (t0) REVERT: B 322 ASP cc_start: 0.6452 (t0) cc_final: 0.6193 (t0) REVERT: B 325 MET cc_start: 0.6915 (tpp) cc_final: 0.6583 (tpp) REVERT: D 56 VAL cc_start: 0.7064 (t) cc_final: 0.6785 (m) REVERT: D 86 SER cc_start: 0.8600 (t) cc_final: 0.8381 (p) REVERT: D 104 LEU cc_start: 0.7932 (mt) cc_final: 0.7703 (mt) REVERT: D 121 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7024 (mtm) REVERT: D 136 SER cc_start: 0.7980 (t) cc_final: 0.7389 (p) outliers start: 33 outliers final: 15 residues processed: 227 average time/residue: 0.2039 time to fit residues: 60.5904 Evaluate side-chains 228 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN D 44 GLN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7344 Z= 0.183 Angle : 0.514 7.849 9962 Z= 0.264 Chirality : 0.041 0.137 1142 Planarity : 0.004 0.056 1261 Dihedral : 5.005 49.562 998 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.99 % Allowed : 16.25 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 905 helix: 1.80 (0.27), residues: 382 sheet: -0.56 (0.34), residues: 193 loop : 0.37 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 324 PHE 0.015 0.001 PHE D 107 TYR 0.009 0.001 TYR B 289 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7414 (mmtt) cc_final: 0.7086 (mmtt) REVERT: A 20 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6251 (mt-10) REVERT: A 186 GLU cc_start: 0.6673 (tt0) cc_final: 0.6430 (tt0) REVERT: A 239 ASP cc_start: 0.7069 (m-30) cc_final: 0.6825 (t0) REVERT: A 276 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6839 (mt-10) REVERT: A 311 GLU cc_start: 0.6302 (mm-30) cc_final: 0.6028 (mm-30) REVERT: A 335 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: B 59 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: B 68 ARG cc_start: 0.7744 (ttt90) cc_final: 0.7349 (ttt90) REVERT: B 83 ASP cc_start: 0.7582 (t0) cc_final: 0.7233 (t70) REVERT: B 101 MET cc_start: 0.7796 (mtp) cc_final: 0.7544 (mtp) REVERT: B 119 ASN cc_start: 0.8348 (m-40) cc_final: 0.8099 (m-40) REVERT: B 136 SER cc_start: 0.7858 (t) cc_final: 0.7524 (p) REVERT: B 150 ARG cc_start: 0.8347 (mmt-90) cc_final: 0.7798 (mmt-90) REVERT: B 189 SER cc_start: 0.8209 (p) cc_final: 0.7918 (p) REVERT: B 196 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7712 (m) REVERT: B 201 SER cc_start: 0.8251 (m) cc_final: 0.8000 (p) REVERT: B 214 ARG cc_start: 0.7321 (mpt90) cc_final: 0.6669 (mpt180) REVERT: B 219 ARG cc_start: 0.7024 (mmt180) cc_final: 0.6567 (mmt-90) REVERT: B 230 ASN cc_start: 0.7429 (t0) cc_final: 0.6916 (m-40) REVERT: B 233 CYS cc_start: 0.7728 (t) cc_final: 0.7377 (t) REVERT: B 243 THR cc_start: 0.7586 (p) cc_final: 0.7376 (p) REVERT: B 297 TRP cc_start: 0.8608 (m100) cc_final: 0.8303 (m100) REVERT: B 304 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7414 (ttm170) REVERT: B 312 ASP cc_start: 0.6519 (t0) cc_final: 0.5864 (t0) REVERT: B 322 ASP cc_start: 0.6506 (t0) cc_final: 0.6226 (t0) REVERT: B 325 MET cc_start: 0.6915 (tpp) cc_final: 0.6574 (tpp) REVERT: D 56 VAL cc_start: 0.7024 (t) cc_final: 0.6754 (m) REVERT: D 86 SER cc_start: 0.8597 (t) cc_final: 0.8372 (p) REVERT: D 104 LEU cc_start: 0.7928 (mt) cc_final: 0.7702 (mt) REVERT: D 121 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7063 (mtt) REVERT: D 136 SER cc_start: 0.8000 (t) cc_final: 0.7444 (p) REVERT: D 195 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6506 (mtm) outliers start: 23 outliers final: 15 residues processed: 210 average time/residue: 0.1993 time to fit residues: 55.0244 Evaluate side-chains 225 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7344 Z= 0.234 Angle : 0.529 8.210 9962 Z= 0.270 Chirality : 0.042 0.136 1142 Planarity : 0.004 0.059 1261 Dihedral : 5.011 49.781 998 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.99 % Allowed : 17.43 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 905 helix: 1.72 (0.27), residues: 384 sheet: -0.63 (0.34), residues: 190 loop : 0.33 (0.38), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 324 PHE 0.017 0.002 PHE A 189 TYR 0.011 0.001 TYR D 176 ARG 0.007 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7469 (mmtt) cc_final: 0.7054 (mmtt) REVERT: A 20 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6304 (mt-10) REVERT: A 31 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7623 (mmm-85) REVERT: A 186 GLU cc_start: 0.6685 (tt0) cc_final: 0.6444 (tt0) REVERT: A 239 ASP cc_start: 0.7046 (m-30) cc_final: 0.6813 (t0) REVERT: A 276 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6830 (mt-10) REVERT: A 311 GLU cc_start: 0.6389 (mm-30) cc_final: 0.6140 (mm-30) REVERT: A 335 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7195 (m-30) REVERT: B 59 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: B 68 ARG cc_start: 0.7755 (ttt90) cc_final: 0.7455 (ttt90) REVERT: B 101 MET cc_start: 0.7794 (mtp) cc_final: 0.7534 (mtp) REVERT: B 136 SER cc_start: 0.7835 (t) cc_final: 0.7498 (p) REVERT: B 139 LEU cc_start: 0.8400 (mt) cc_final: 0.8175 (mt) REVERT: B 145 TYR cc_start: 0.8235 (p90) cc_final: 0.7389 (p90) REVERT: B 147 SER cc_start: 0.8089 (t) cc_final: 0.7852 (p) REVERT: B 150 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.7806 (mmt-90) REVERT: B 189 SER cc_start: 0.8139 (p) cc_final: 0.7868 (p) REVERT: B 196 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7741 (m) REVERT: B 201 SER cc_start: 0.8270 (m) cc_final: 0.8062 (p) REVERT: B 214 ARG cc_start: 0.7394 (mpt90) cc_final: 0.6750 (mpt180) REVERT: B 219 ARG cc_start: 0.7002 (mmt180) cc_final: 0.6506 (mmt-90) REVERT: B 230 ASN cc_start: 0.7313 (t0) cc_final: 0.6991 (m-40) REVERT: B 233 CYS cc_start: 0.7760 (t) cc_final: 0.7388 (t) REVERT: B 277 SER cc_start: 0.8054 (t) cc_final: 0.7468 (m) REVERT: B 297 TRP cc_start: 0.8598 (m100) cc_final: 0.8336 (m100) REVERT: B 304 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7599 (ttm170) REVERT: B 322 ASP cc_start: 0.6651 (t0) cc_final: 0.6367 (t0) REVERT: B 325 MET cc_start: 0.6877 (tpp) cc_final: 0.6551 (tpp) REVERT: D 56 VAL cc_start: 0.7067 (t) cc_final: 0.6787 (m) REVERT: D 86 SER cc_start: 0.8578 (t) cc_final: 0.8335 (p) REVERT: D 121 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7056 (mtm) REVERT: D 136 SER cc_start: 0.8037 (t) cc_final: 0.7475 (p) REVERT: D 182 LEU cc_start: 0.8158 (tp) cc_final: 0.7940 (tt) REVERT: P 6 MET cc_start: 0.7591 (mtp) cc_final: 0.7099 (mtm) outliers start: 23 outliers final: 14 residues processed: 213 average time/residue: 0.1998 time to fit residues: 56.2594 Evaluate side-chains 220 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7344 Z= 0.224 Angle : 0.538 8.927 9962 Z= 0.273 Chirality : 0.042 0.145 1142 Planarity : 0.004 0.059 1261 Dihedral : 4.951 49.628 998 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.38 % Allowed : 17.82 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 905 helix: 1.84 (0.27), residues: 381 sheet: -0.66 (0.34), residues: 191 loop : 0.32 (0.38), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.017 0.001 PHE A 189 TYR 0.009 0.001 TYR B 289 ARG 0.006 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7090 (mmtt) REVERT: A 20 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6302 (mt-10) REVERT: A 31 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: A 186 GLU cc_start: 0.6691 (tt0) cc_final: 0.6441 (tt0) REVERT: A 239 ASP cc_start: 0.7087 (m-30) cc_final: 0.6824 (t0) REVERT: A 311 GLU cc_start: 0.6399 (mm-30) cc_final: 0.6180 (mm-30) REVERT: A 335 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: B 59 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: B 68 ARG cc_start: 0.7765 (ttt90) cc_final: 0.7363 (ttt90) REVERT: B 101 MET cc_start: 0.7770 (mtp) cc_final: 0.7443 (mtp) REVERT: B 136 SER cc_start: 0.7678 (t) cc_final: 0.7335 (p) REVERT: B 139 LEU cc_start: 0.8397 (mt) cc_final: 0.8173 (mt) REVERT: B 145 TYR cc_start: 0.8245 (p90) cc_final: 0.7427 (p90) REVERT: B 150 ARG cc_start: 0.8375 (mmt-90) cc_final: 0.7828 (mmt-90) REVERT: B 189 SER cc_start: 0.8176 (p) cc_final: 0.7880 (p) REVERT: B 196 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7708 (m) REVERT: B 214 ARG cc_start: 0.7419 (mpt90) cc_final: 0.6859 (mpt180) REVERT: B 219 ARG cc_start: 0.6982 (mmt180) cc_final: 0.6497 (mmt-90) REVERT: B 230 ASN cc_start: 0.7259 (t0) cc_final: 0.7023 (m-40) REVERT: B 233 CYS cc_start: 0.7682 (t) cc_final: 0.7362 (t) REVERT: B 277 SER cc_start: 0.8038 (t) cc_final: 0.7442 (m) REVERT: B 297 TRP cc_start: 0.8590 (m100) cc_final: 0.8354 (m100) REVERT: B 304 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7618 (ttm170) REVERT: B 322 ASP cc_start: 0.6712 (t0) cc_final: 0.6429 (t0) REVERT: D 56 VAL cc_start: 0.7077 (t) cc_final: 0.6790 (m) REVERT: D 72 MET cc_start: 0.6458 (ttm) cc_final: 0.6256 (ttm) REVERT: D 86 SER cc_start: 0.8563 (t) cc_final: 0.8326 (p) REVERT: D 121 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7050 (mtm) REVERT: D 136 SER cc_start: 0.8036 (t) cc_final: 0.7497 (p) REVERT: D 182 LEU cc_start: 0.7905 (tp) cc_final: 0.7693 (tt) outliers start: 26 outliers final: 15 residues processed: 212 average time/residue: 0.2036 time to fit residues: 57.0289 Evaluate side-chains 220 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.0060 chunk 42 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7344 Z= 0.159 Angle : 0.526 10.655 9962 Z= 0.264 Chirality : 0.041 0.142 1142 Planarity : 0.004 0.051 1261 Dihedral : 4.798 49.189 998 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.47 % Allowed : 18.99 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 905 helix: 2.01 (0.27), residues: 382 sheet: -0.62 (0.33), residues: 193 loop : 0.37 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 324 PHE 0.012 0.001 PHE A 189 TYR 0.009 0.001 TYR A 306 ARG 0.009 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 0.740 Fit side-chains REVERT: A 20 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6495 (mt-10) REVERT: A 35 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7965 (mtm-85) REVERT: A 186 GLU cc_start: 0.6627 (tt0) cc_final: 0.6389 (tt0) REVERT: A 239 ASP cc_start: 0.7062 (m-30) cc_final: 0.6805 (t0) REVERT: A 311 GLU cc_start: 0.6316 (mm-30) cc_final: 0.5876 (mm-30) REVERT: A 335 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: B 68 ARG cc_start: 0.7583 (ttt90) cc_final: 0.7221 (ttm-80) REVERT: B 83 ASP cc_start: 0.7630 (t0) cc_final: 0.6855 (t0) REVERT: B 86 THR cc_start: 0.8168 (p) cc_final: 0.7943 (p) REVERT: B 101 MET cc_start: 0.7737 (mtp) cc_final: 0.7417 (mtp) REVERT: B 119 ASN cc_start: 0.8398 (m-40) cc_final: 0.8098 (m-40) REVERT: B 136 SER cc_start: 0.7584 (t) cc_final: 0.7232 (p) REVERT: B 145 TYR cc_start: 0.8147 (p90) cc_final: 0.7334 (p90) REVERT: B 150 ARG cc_start: 0.8340 (mmt-90) cc_final: 0.7802 (mmt-90) REVERT: B 189 SER cc_start: 0.8197 (p) cc_final: 0.7897 (p) REVERT: B 191 SER cc_start: 0.8114 (p) cc_final: 0.7888 (p) REVERT: B 196 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7623 (m) REVERT: B 214 ARG cc_start: 0.7457 (mpt90) cc_final: 0.6855 (mpt180) REVERT: B 219 ARG cc_start: 0.7003 (mmt180) cc_final: 0.6480 (mmt-90) REVERT: B 230 ASN cc_start: 0.7188 (t0) cc_final: 0.6963 (m-40) REVERT: B 233 CYS cc_start: 0.7683 (t) cc_final: 0.7379 (t) REVERT: B 243 THR cc_start: 0.7567 (p) cc_final: 0.7307 (p) REVERT: B 277 SER cc_start: 0.7982 (t) cc_final: 0.7352 (m) REVERT: B 304 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7598 (ttm170) REVERT: B 322 ASP cc_start: 0.6709 (t0) cc_final: 0.6453 (t0) REVERT: B 325 MET cc_start: 0.6847 (tpp) cc_final: 0.6533 (tpp) REVERT: D 56 VAL cc_start: 0.7046 (t) cc_final: 0.6747 (m) REVERT: D 86 SER cc_start: 0.8564 (t) cc_final: 0.8350 (p) REVERT: D 121 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7074 (mtt) REVERT: D 136 SER cc_start: 0.8007 (t) cc_final: 0.7468 (p) REVERT: D 202 ASN cc_start: 0.7476 (t0) cc_final: 0.7217 (t0) outliers start: 19 outliers final: 12 residues processed: 206 average time/residue: 0.2269 time to fit residues: 59.5376 Evaluate side-chains 201 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7344 Z= 0.286 Angle : 0.573 12.101 9962 Z= 0.286 Chirality : 0.043 0.153 1142 Planarity : 0.004 0.056 1261 Dihedral : 4.749 29.712 996 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.25 % Allowed : 18.73 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 905 helix: 1.82 (0.27), residues: 386 sheet: -0.71 (0.33), residues: 195 loop : 0.24 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.004 0.001 HIS A 324 PHE 0.018 0.002 PHE A 189 TYR 0.012 0.001 TYR D 176 ARG 0.010 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7396 (mmtt) cc_final: 0.7024 (mmtt) REVERT: A 20 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6376 (mt-10) REVERT: A 186 GLU cc_start: 0.6696 (tt0) cc_final: 0.6440 (tt0) REVERT: A 239 ASP cc_start: 0.7084 (m-30) cc_final: 0.6811 (t0) REVERT: A 311 GLU cc_start: 0.6476 (mm-30) cc_final: 0.6250 (mm-30) REVERT: A 335 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7195 (m-30) REVERT: B 68 ARG cc_start: 0.7722 (ttt90) cc_final: 0.7476 (ttm-80) REVERT: B 101 MET cc_start: 0.7768 (mtp) cc_final: 0.7455 (mtp) REVERT: B 119 ASN cc_start: 0.8565 (m-40) cc_final: 0.8264 (m-40) REVERT: B 136 SER cc_start: 0.7671 (t) cc_final: 0.7313 (p) REVERT: B 147 SER cc_start: 0.8159 (t) cc_final: 0.7865 (p) REVERT: B 149 CYS cc_start: 0.7285 (p) cc_final: 0.6656 (p) REVERT: B 150 ARG cc_start: 0.8376 (mmt-90) cc_final: 0.7947 (mmt-90) REVERT: B 189 SER cc_start: 0.8162 (p) cc_final: 0.7808 (p) REVERT: B 196 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7670 (m) REVERT: B 214 ARG cc_start: 0.7526 (mpt90) cc_final: 0.6979 (mpt180) REVERT: B 219 ARG cc_start: 0.7028 (mmt180) cc_final: 0.6502 (mmt-90) REVERT: B 230 ASN cc_start: 0.7209 (t0) cc_final: 0.6875 (m-40) REVERT: B 233 CYS cc_start: 0.7717 (t) cc_final: 0.7386 (t) REVERT: B 243 THR cc_start: 0.7608 (p) cc_final: 0.7359 (p) REVERT: B 277 SER cc_start: 0.8067 (t) cc_final: 0.7472 (m) REVERT: B 297 TRP cc_start: 0.8559 (m100) cc_final: 0.8302 (m100) REVERT: B 304 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7608 (ttm170) REVERT: B 322 ASP cc_start: 0.6762 (t0) cc_final: 0.6463 (t0) REVERT: B 325 MET cc_start: 0.6854 (tpp) cc_final: 0.6563 (tpp) REVERT: D 56 VAL cc_start: 0.7102 (t) cc_final: 0.6824 (m) REVERT: D 86 SER cc_start: 0.8549 (t) cc_final: 0.8315 (p) REVERT: D 98 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7955 (m110) REVERT: D 121 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7108 (mtm) REVERT: D 136 SER cc_start: 0.8029 (t) cc_final: 0.7456 (p) REVERT: D 202 ASN cc_start: 0.7558 (t0) cc_final: 0.7326 (t0) REVERT: D 309 LYS cc_start: 0.7864 (mtmt) cc_final: 0.7598 (mmmm) outliers start: 25 outliers final: 17 residues processed: 220 average time/residue: 0.2289 time to fit residues: 65.3868 Evaluate side-chains 226 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7344 Z= 0.217 Angle : 0.559 12.139 9962 Z= 0.279 Chirality : 0.043 0.160 1142 Planarity : 0.004 0.055 1261 Dihedral : 4.671 27.790 996 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.86 % Allowed : 19.77 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 905 helix: 1.89 (0.27), residues: 382 sheet: -0.76 (0.33), residues: 193 loop : 0.20 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 324 PHE 0.018 0.001 PHE D 198 TYR 0.009 0.001 TYR D 176 ARG 0.009 0.001 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7383 (mmtt) cc_final: 0.7018 (mmtt) REVERT: A 20 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6384 (mt-10) REVERT: A 26 ASP cc_start: 0.6687 (m-30) cc_final: 0.6323 (m-30) REVERT: A 186 GLU cc_start: 0.6668 (tt0) cc_final: 0.6410 (tt0) REVERT: A 239 ASP cc_start: 0.7068 (m-30) cc_final: 0.6822 (t0) REVERT: A 311 GLU cc_start: 0.6378 (mm-30) cc_final: 0.6163 (mm-30) REVERT: B 68 ARG cc_start: 0.7664 (ttt90) cc_final: 0.7434 (ttm-80) REVERT: B 101 MET cc_start: 0.7737 (mtp) cc_final: 0.7432 (mtp) REVERT: B 119 ASN cc_start: 0.8546 (m-40) cc_final: 0.8238 (m-40) REVERT: B 136 SER cc_start: 0.7643 (t) cc_final: 0.7288 (p) REVERT: B 145 TYR cc_start: 0.8221 (p90) cc_final: 0.7404 (p90) REVERT: B 149 CYS cc_start: 0.7299 (p) cc_final: 0.6657 (p) REVERT: B 150 ARG cc_start: 0.8356 (mmt-90) cc_final: 0.7957 (mmt-90) REVERT: B 158 VAL cc_start: 0.8012 (t) cc_final: 0.7746 (p) REVERT: B 189 SER cc_start: 0.8170 (p) cc_final: 0.7829 (p) REVERT: B 191 SER cc_start: 0.8112 (p) cc_final: 0.7741 (t) REVERT: B 196 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7680 (m) REVERT: B 214 ARG cc_start: 0.7548 (mpt90) cc_final: 0.6949 (mpt180) REVERT: B 219 ARG cc_start: 0.7018 (mmt180) cc_final: 0.6503 (mmt-90) REVERT: B 230 ASN cc_start: 0.7158 (t0) cc_final: 0.6916 (m-40) REVERT: B 233 CYS cc_start: 0.7788 (t) cc_final: 0.7380 (t) REVERT: B 243 THR cc_start: 0.7598 (p) cc_final: 0.7359 (p) REVERT: B 277 SER cc_start: 0.8029 (t) cc_final: 0.7434 (m) REVERT: B 297 TRP cc_start: 0.8557 (m100) cc_final: 0.8302 (m100) REVERT: B 304 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7605 (ttm170) REVERT: B 325 MET cc_start: 0.6815 (tpp) cc_final: 0.6519 (tpp) REVERT: D 56 VAL cc_start: 0.7104 (t) cc_final: 0.6823 (m) REVERT: D 86 SER cc_start: 0.8542 (t) cc_final: 0.8320 (p) REVERT: D 121 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7054 (mtm) REVERT: D 136 SER cc_start: 0.7917 (t) cc_final: 0.7626 (t) REVERT: D 137 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7543 (mt) outliers start: 22 outliers final: 17 residues processed: 207 average time/residue: 0.2129 time to fit residues: 58.4601 Evaluate side-chains 216 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120335 restraints weight = 9699.379| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.18 r_work: 0.3345 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7344 Z= 0.195 Angle : 0.541 11.205 9962 Z= 0.272 Chirality : 0.042 0.156 1142 Planarity : 0.004 0.051 1261 Dihedral : 4.588 26.349 996 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.73 % Allowed : 19.90 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 905 helix: 1.94 (0.27), residues: 381 sheet: -0.74 (0.32), residues: 199 loop : 0.24 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS A 324 PHE 0.019 0.001 PHE D 198 TYR 0.008 0.001 TYR A 306 ARG 0.009 0.001 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.69 seconds wall clock time: 39 minutes 51.00 seconds (2391.00 seconds total)