Starting phenix.real_space_refine on Mon Mar 11 14:33:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvp_22509/03_2024/7jvp_22509_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvp_22509/03_2024/7jvp_22509.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvp_22509/03_2024/7jvp_22509_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvp_22509/03_2024/7jvp_22509_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvp_22509/03_2024/7jvp_22509_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvp_22509/03_2024/7jvp_22509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvp_22509/03_2024/7jvp_22509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvp_22509/03_2024/7jvp_22509_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvp_22509/03_2024/7jvp_22509_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 1 4.86 5 C 5462 2.51 5 N 1440 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 23": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 130": "NH1" <-> "NH2" Residue "R ARG 133": "NH1" <-> "NH2" Residue "R ARG 216": "NH1" <-> "NH2" Residue "R ARG 219": "NH1" <-> "NH2" Residue "R ARG 226": "NH1" <-> "NH2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 266": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 105": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8486 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2227 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 3 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1966 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2604 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 280 Unusual residues: {'CLR': 6, 'PLM': 5, 'SK9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 5.34, per 1000 atoms: 0.63 Number of scatterers: 8486 At special positions: 0 Unit cell: (97.185, 106.59, 122.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 53 16.00 O 1530 8.00 N 1440 7.00 C 5462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 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: 3.44 Conformation dependent library (CDL) restraints added in 1.7 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 41.3% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'R' and resid 21 through 50 Processing helix chain 'R' and resid 52 through 56 Processing helix chain 'R' and resid 59 through 76 removed outlier: 3.961A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 94 through 126 removed outlier: 3.793A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS R 106 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER R 107 " --> pdb=" O ILE R 104 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR R 108 " --> pdb=" O MET R 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU R 112 " --> pdb=" O ALA R 109 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE R 125 " --> pdb=" O TYR R 122 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER R 126 " --> pdb=" O TRP R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 Processing helix chain 'R' and resid 137 through 160 removed outlier: 4.141A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 192 through 202 Processing helix chain 'R' and resid 204 through 238 Processing helix chain 'R' and resid 265 through 298 Proline residue: R 287 - end of helix Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 310 through 331 removed outlier: 3.598A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 345 Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.877A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 240' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 332 through 352 Processing helix chain 'A' and resid 369 through 390 removed outlier: 3.901A pdb=" N ILE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.199A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.237A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.063A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.846A 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: 6.708A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.571A 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: 6.435A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.901A 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: 6.948A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.813A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.947A 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: 6.520A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.957A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.639A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1098 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: 2.54 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2656 1.34 - 1.46: 1951 1.46 - 1.58: 3987 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8667 Sorted by residual: bond pdb=" C04 SK9 R 501 " pdb="CL01 SK9 R 501 " ideal model delta sigma weight residual 1.785 1.714 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C02 SK9 R 501 " pdb=" O02 SK9 R 501 " ideal model delta sigma weight residual 1.401 1.354 0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" N LEU R 291 " pdb=" CA LEU R 291 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.36e+00 bond pdb=" C01 SK9 R 501 " pdb=" O01 SK9 R 501 " ideal model delta sigma weight residual 1.401 1.357 0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" N PHE R 313 " pdb=" CA PHE R 313 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.74e+00 ... (remaining 8662 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.57: 229 106.57 - 113.45: 4852 113.45 - 120.33: 3156 120.33 - 127.20: 3409 127.20 - 134.08: 95 Bond angle restraints: 11741 Sorted by residual: angle pdb=" C CYS A 365 " pdb=" N SER A 366 " pdb=" CA SER A 366 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C05 SK9 R 501 " pdb=" C06 SK9 R 501 " pdb=" C08 SK9 R 501 " ideal model delta sigma weight residual 111.00 124.10 -13.10 3.00e+00 1.11e-01 1.91e+01 angle pdb=" N LEU R 295 " pdb=" CA LEU R 295 " pdb=" C LEU R 295 " ideal model delta sigma weight residual 113.16 118.65 -5.49 1.42e+00 4.96e-01 1.49e+01 angle pdb=" C CYS B 250 " pdb=" N ARG B 251 " pdb=" CA ARG B 251 " ideal model delta sigma weight residual 122.99 117.69 5.30 1.41e+00 5.03e-01 1.41e+01 angle pdb=" C07 SK9 R 501 " pdb=" C09 SK9 R 501 " pdb=" N01 SK9 R 501 " ideal model delta sigma weight residual 112.96 124.10 -11.14 3.00e+00 1.11e-01 1.38e+01 ... (remaining 11736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.38: 5420 32.38 - 64.77: 41 64.77 - 97.15: 3 97.15 - 129.53: 1 129.53 - 161.92: 1 Dihedral angle restraints: 5466 sinusoidal: 2437 harmonic: 3029 Sorted by residual: dihedral pdb=" C06 SK9 R 501 " pdb=" C08 SK9 R 501 " pdb=" C10 SK9 R 501 " pdb=" N01 SK9 R 501 " ideal model delta sinusoidal sigma weight residual 74.51 -87.41 161.92 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C04 SK9 R 501 " pdb=" C06 SK9 R 501 " pdb=" C08 SK9 R 501 " pdb=" C10 SK9 R 501 " ideal model delta sinusoidal sigma weight residual 116.94 -116.12 -126.94 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 5463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1133 0.087 - 0.174: 164 0.174 - 0.261: 21 0.261 - 0.348: 6 0.348 - 0.435: 6 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 1327 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 380 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ARG A 380 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG A 380 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A 381 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 375 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C VAL A 375 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL A 375 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 376 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.049 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO A 361 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.041 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 486 2.75 - 3.28: 8347 3.28 - 3.82: 14245 3.82 - 4.36: 16983 4.36 - 4.90: 29464 Nonbonded interactions: 69525 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.208 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.225 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.254 2.440 nonbonded pdb=" O SER R 198 " pdb=" OG SER R 202 " model vdw 2.264 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.268 2.440 ... (remaining 69520 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: 0.400 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: 2.220 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.400 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.005 0.071 8667 Z= 0.332 Angle : 0.973 13.104 11741 Z= 0.537 Chirality : 0.069 0.435 1330 Planarity : 0.007 0.075 1447 Dihedral : 9.734 161.917 3489 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 2.55 (0.24), residues: 1021 helix: 3.52 (0.21), residues: 423 sheet: 2.92 (0.34), residues: 196 loop : -1.16 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 281 HIS 0.019 0.004 HIS A 220 PHE 0.041 0.004 PHE B 234 TYR 0.023 0.003 TYR A 311 ARG 0.018 0.001 ARG R 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 278 MET cc_start: 0.7523 (mmm) cc_final: 0.7254 (mmp) REVERT: A 17 LYS cc_start: 0.7640 (tttt) cc_final: 0.7074 (mmmt) REVERT: A 378 ASP cc_start: 0.7661 (m-30) cc_final: 0.7406 (m-30) REVERT: B 161 SER cc_start: 0.8590 (t) cc_final: 0.8083 (m) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 1.1370 time to fit residues: 299.0195 Evaluate side-chains 149 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 53 HIS ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 384 GLN B 6 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 110 ASN B 259 GLN N 31 ASN N 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8667 Z= 0.230 Angle : 0.544 6.802 11741 Z= 0.293 Chirality : 0.042 0.143 1330 Planarity : 0.005 0.049 1447 Dihedral : 8.663 165.738 1597 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.35 % Allowed : 13.10 % Favored : 84.55 % 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: 1.97 (0.24), residues: 1021 helix: 2.75 (0.22), residues: 421 sheet: 1.54 (0.33), residues: 212 loop : -0.51 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 281 HIS 0.010 0.002 HIS A 357 PHE 0.016 0.002 PHE R 288 TYR 0.017 0.002 TYR B 59 ARG 0.007 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 0.908 Fit side-chains REVERT: R 50 ARG cc_start: 0.6284 (mmt90) cc_final: 0.5995 (tpp-160) REVERT: R 59 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8702 (p) REVERT: R 278 MET cc_start: 0.7802 (mmm) cc_final: 0.7517 (mmp) REVERT: A 17 LYS cc_start: 0.7678 (tttt) cc_final: 0.7077 (mmmt) REVERT: A 53 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6819 (mtmt) REVERT: A 319 THR cc_start: 0.7727 (t) cc_final: 0.7493 (m) REVERT: A 378 ASP cc_start: 0.7813 (m-30) cc_final: 0.7460 (m-30) REVERT: A 386 MET cc_start: 0.7587 (ttm) cc_final: 0.7313 (ttp) REVERT: B 78 LYS cc_start: 0.8837 (tppt) cc_final: 0.8635 (tppt) outliers start: 21 outliers final: 8 residues processed: 202 average time/residue: 1.2389 time to fit residues: 265.5769 Evaluate side-chains 160 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8667 Z= 0.211 Angle : 0.509 7.138 11741 Z= 0.271 Chirality : 0.040 0.139 1330 Planarity : 0.004 0.041 1447 Dihedral : 8.422 163.191 1597 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.25 % Allowed : 15.90 % Favored : 80.85 % 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: 1.60 (0.25), residues: 1021 helix: 2.32 (0.24), residues: 416 sheet: 1.07 (0.31), residues: 217 loop : -0.33 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.009 0.001 HIS A 357 PHE 0.026 0.002 PHE R 297 TYR 0.014 0.001 TYR R 194 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 0.937 Fit side-chains REVERT: R 154 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7875 (tt) REVERT: R 333 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7323 (m-10) REVERT: A 17 LYS cc_start: 0.7635 (tttt) cc_final: 0.7059 (mmmt) REVERT: A 53 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6905 (mtmt) REVERT: A 265 ARG cc_start: 0.7463 (ptt180) cc_final: 0.7232 (ppt-90) REVERT: A 378 ASP cc_start: 0.7776 (m-30) cc_final: 0.7366 (m-30) REVERT: A 386 MET cc_start: 0.7524 (ttm) cc_final: 0.7268 (ttp) REVERT: B 188 MET cc_start: 0.8493 (mmm) cc_final: 0.8242 (mmm) outliers start: 29 outliers final: 16 residues processed: 173 average time/residue: 1.3064 time to fit residues: 240.2083 Evaluate side-chains 158 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 292 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 156 GLN B 220 GLN B 259 GLN N 31 ASN N 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8667 Z= 0.316 Angle : 0.557 7.877 11741 Z= 0.297 Chirality : 0.042 0.134 1330 Planarity : 0.005 0.060 1447 Dihedral : 8.605 163.798 1597 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.03 % Allowed : 16.69 % Favored : 79.28 % 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: 1.15 (0.25), residues: 1021 helix: 1.73 (0.24), residues: 424 sheet: 0.59 (0.31), residues: 214 loop : -0.13 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.013 0.002 HIS A 357 PHE 0.024 0.002 PHE R 288 TYR 0.016 0.002 TYR R 194 ARG 0.010 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 0.930 Fit side-chains REVERT: R 36 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8400 (m) REVERT: A 17 LYS cc_start: 0.7673 (tttt) cc_final: 0.7108 (mmmt) REVERT: A 53 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7123 (ttpt) REVERT: A 370 GLU cc_start: 0.7267 (pm20) cc_final: 0.6850 (pm20) REVERT: A 378 ASP cc_start: 0.7782 (m-30) cc_final: 0.7433 (m-30) REVERT: A 386 MET cc_start: 0.7474 (ttm) cc_final: 0.7194 (ttp) REVERT: B 32 GLN cc_start: 0.8612 (mt0) cc_final: 0.8389 (mt0) REVERT: B 258 ASP cc_start: 0.8097 (t0) cc_final: 0.7683 (t0) REVERT: N 38 ARG cc_start: 0.8381 (ptt-90) cc_final: 0.8140 (ptp90) outliers start: 36 outliers final: 18 residues processed: 172 average time/residue: 1.3813 time to fit residues: 250.8186 Evaluate side-chains 152 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8667 Z= 0.310 Angle : 0.552 7.140 11741 Z= 0.292 Chirality : 0.042 0.135 1330 Planarity : 0.005 0.066 1447 Dihedral : 8.784 163.980 1597 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.93 % Allowed : 17.02 % Favored : 78.05 % 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: 0.94 (0.25), residues: 1021 helix: 1.68 (0.24), residues: 416 sheet: 0.12 (0.31), residues: 213 loop : -0.12 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.010 0.002 HIS A 357 PHE 0.024 0.002 PHE R 288 TYR 0.014 0.002 TYR R 194 ARG 0.009 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 139 time to evaluate : 0.978 Fit side-chains REVERT: R 36 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8513 (m) REVERT: R 213 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8146 (p) REVERT: A 17 LYS cc_start: 0.7704 (tttt) cc_final: 0.7124 (mmmt) REVERT: A 53 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7159 (ttpt) REVERT: A 370 GLU cc_start: 0.7340 (pm20) cc_final: 0.7105 (pm20) REVERT: A 378 ASP cc_start: 0.7792 (m-30) cc_final: 0.7424 (m-30) REVERT: A 386 MET cc_start: 0.7499 (ttm) cc_final: 0.7230 (ttp) REVERT: B 32 GLN cc_start: 0.8649 (mt0) cc_final: 0.8358 (mt0) REVERT: B 258 ASP cc_start: 0.8143 (t0) cc_final: 0.7717 (t0) REVERT: N 90 ASP cc_start: 0.8539 (m-30) cc_final: 0.8298 (m-30) REVERT: N 110 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8631 (m) outliers start: 44 outliers final: 21 residues processed: 165 average time/residue: 1.3202 time to fit residues: 230.7651 Evaluate side-chains 153 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.0040 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8667 Z= 0.189 Angle : 0.488 6.632 11741 Z= 0.259 Chirality : 0.039 0.136 1330 Planarity : 0.004 0.048 1447 Dihedral : 8.449 162.788 1597 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.37 % Allowed : 18.48 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1021 helix: 1.73 (0.24), residues: 424 sheet: -0.26 (0.30), residues: 224 loop : -0.07 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.001 PHE R 288 TYR 0.013 0.001 TYR N 60 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 0.984 Fit side-chains REVERT: R 213 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8140 (p) REVERT: A 17 LYS cc_start: 0.7735 (tttt) cc_final: 0.7145 (mmmt) REVERT: A 378 ASP cc_start: 0.7778 (m-30) cc_final: 0.7410 (m-30) REVERT: A 386 MET cc_start: 0.7486 (ttm) cc_final: 0.7216 (ttp) REVERT: B 32 GLN cc_start: 0.8600 (mt0) cc_final: 0.8356 (mt0) REVERT: B 146 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8583 (mp) REVERT: B 258 ASP cc_start: 0.8098 (t0) cc_final: 0.7528 (t0) REVERT: N 3 GLN cc_start: 0.7835 (pt0) cc_final: 0.7613 (tt0) REVERT: N 110 VAL cc_start: 0.8932 (t) cc_final: 0.8493 (m) outliers start: 39 outliers final: 27 residues processed: 161 average time/residue: 1.2849 time to fit residues: 219.6278 Evaluate side-chains 159 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 54 optimal weight: 0.0370 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8667 Z= 0.213 Angle : 0.498 6.823 11741 Z= 0.264 Chirality : 0.039 0.138 1330 Planarity : 0.004 0.051 1447 Dihedral : 8.393 162.930 1597 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.70 % Allowed : 18.92 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1021 helix: 1.71 (0.24), residues: 425 sheet: -0.34 (0.30), residues: 224 loop : -0.06 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.001 PHE R 288 TYR 0.015 0.001 TYR N 60 ARG 0.012 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 0.944 Fit side-chains REVERT: R 36 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8493 (m) REVERT: R 213 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8133 (p) REVERT: A 17 LYS cc_start: 0.7733 (tttt) cc_final: 0.7142 (mmmt) REVERT: A 378 ASP cc_start: 0.7777 (m-30) cc_final: 0.7425 (m-30) REVERT: A 386 MET cc_start: 0.7505 (ttm) cc_final: 0.7242 (ttp) REVERT: A 392 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 32 GLN cc_start: 0.8621 (mt0) cc_final: 0.8366 (mt0) REVERT: B 146 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8569 (mp) REVERT: B 258 ASP cc_start: 0.8117 (t0) cc_final: 0.7513 (t0) REVERT: N 3 GLN cc_start: 0.7825 (pt0) cc_final: 0.7414 (tt0) REVERT: N 35 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7759 (p0) REVERT: N 110 VAL cc_start: 0.8932 (t) cc_final: 0.8444 (m) outliers start: 33 outliers final: 25 residues processed: 159 average time/residue: 1.2191 time to fit residues: 206.8716 Evaluate side-chains 160 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8667 Z= 0.203 Angle : 0.499 6.747 11741 Z= 0.264 Chirality : 0.039 0.138 1330 Planarity : 0.004 0.053 1447 Dihedral : 8.298 162.755 1597 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.81 % Allowed : 19.04 % Favored : 77.16 % 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: 0.81 (0.26), residues: 1021 helix: 1.65 (0.24), residues: 430 sheet: -0.37 (0.30), residues: 220 loop : -0.08 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.001 PHE R 288 TYR 0.017 0.001 TYR N 60 ARG 0.008 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 0.927 Fit side-chains REVERT: R 36 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8538 (m) REVERT: R 92 PHE cc_start: 0.3711 (m-80) cc_final: 0.3169 (m-80) REVERT: R 213 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8128 (p) REVERT: A 17 LYS cc_start: 0.7790 (tttt) cc_final: 0.7165 (mmmt) REVERT: A 378 ASP cc_start: 0.7796 (m-30) cc_final: 0.7462 (m-30) REVERT: A 386 MET cc_start: 0.7523 (ttm) cc_final: 0.7262 (ttp) REVERT: B 32 GLN cc_start: 0.8625 (mt0) cc_final: 0.8379 (mt0) REVERT: B 146 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8553 (mp) REVERT: B 258 ASP cc_start: 0.8144 (t0) cc_final: 0.7484 (t0) REVERT: N 3 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: N 110 VAL cc_start: 0.8893 (t) cc_final: 0.8445 (m) outliers start: 34 outliers final: 27 residues processed: 163 average time/residue: 1.2209 time to fit residues: 211.5945 Evaluate side-chains 165 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8667 Z= 0.191 Angle : 0.497 6.707 11741 Z= 0.263 Chirality : 0.039 0.139 1330 Planarity : 0.004 0.050 1447 Dihedral : 8.243 162.660 1597 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.58 % Allowed : 20.27 % Favored : 76.15 % 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: 0.81 (0.26), residues: 1021 helix: 1.67 (0.24), residues: 430 sheet: -0.40 (0.31), residues: 220 loop : -0.06 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.020 0.001 PHE R 288 TYR 0.018 0.001 TYR N 60 ARG 0.006 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 0.873 Fit side-chains REVERT: R 36 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8534 (m) REVERT: R 92 PHE cc_start: 0.3835 (m-80) cc_final: 0.3243 (m-80) REVERT: R 213 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8137 (p) REVERT: A 17 LYS cc_start: 0.7790 (tttt) cc_final: 0.7148 (mmmt) REVERT: A 378 ASP cc_start: 0.7781 (m-30) cc_final: 0.7355 (m-30) REVERT: A 386 MET cc_start: 0.7521 (ttm) cc_final: 0.7255 (ttp) REVERT: B 146 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 258 ASP cc_start: 0.8135 (t0) cc_final: 0.7494 (t0) REVERT: N 3 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: N 35 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7723 (p0) REVERT: N 110 VAL cc_start: 0.8896 (t) cc_final: 0.8413 (m) outliers start: 32 outliers final: 26 residues processed: 153 average time/residue: 1.2673 time to fit residues: 205.5988 Evaluate side-chains 160 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8667 Z= 0.217 Angle : 0.508 6.878 11741 Z= 0.269 Chirality : 0.039 0.136 1330 Planarity : 0.004 0.052 1447 Dihedral : 8.297 162.950 1597 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.58 % Allowed : 20.49 % Favored : 75.92 % 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: 0.77 (0.26), residues: 1021 helix: 1.67 (0.24), residues: 428 sheet: -0.48 (0.31), residues: 214 loop : -0.09 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.001 PHE R 288 TYR 0.016 0.001 TYR N 60 ARG 0.006 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 0.983 Fit side-chains REVERT: R 36 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8558 (m) REVERT: R 92 PHE cc_start: 0.3977 (m-80) cc_final: 0.3312 (m-80) REVERT: R 213 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8127 (p) REVERT: A 17 LYS cc_start: 0.7775 (tttt) cc_final: 0.7121 (mmmt) REVERT: A 378 ASP cc_start: 0.7792 (m-30) cc_final: 0.7486 (m-30) REVERT: A 386 MET cc_start: 0.7534 (ttm) cc_final: 0.7267 (ttp) REVERT: B 32 GLN cc_start: 0.8642 (mt0) cc_final: 0.8407 (mt0) REVERT: B 146 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8559 (mp) REVERT: B 220 GLN cc_start: 0.8518 (mt0) cc_final: 0.8308 (mt0) REVERT: B 258 ASP cc_start: 0.8159 (t0) cc_final: 0.7461 (t0) REVERT: N 3 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: N 110 VAL cc_start: 0.8933 (t) cc_final: 0.8634 (m) outliers start: 32 outliers final: 28 residues processed: 154 average time/residue: 1.2875 time to fit residues: 210.3767 Evaluate side-chains 162 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.146959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111556 restraints weight = 9529.292| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.96 r_work: 0.3093 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8667 Z= 0.218 Angle : 0.509 6.859 11741 Z= 0.269 Chirality : 0.040 0.137 1330 Planarity : 0.004 0.051 1447 Dihedral : 8.325 163.181 1597 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.58 % Allowed : 20.60 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1021 helix: 1.68 (0.24), residues: 428 sheet: -0.52 (0.32), residues: 214 loop : -0.08 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.020 0.001 PHE R 288 TYR 0.017 0.001 TYR N 60 ARG 0.006 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3980.66 seconds wall clock time: 71 minutes 12.92 seconds (4272.92 seconds total)