Starting phenix.real_space_refine on Wed Sep 25 03:57:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/09_2024/6omm_20126.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/09_2024/6omm_20126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/09_2024/6omm_20126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/09_2024/6omm_20126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/09_2024/6omm_20126.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/09_2024/6omm_20126.cif" } resolution = 3.17 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= 0.005 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 65 5.16 5 C 5907 2.51 5 N 1510 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9134 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2341 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 59 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1754 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 194 Unusual residues: {'CLR': 5, 'PLM': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 6.10, per 1000 atoms: 0.67 Number of scatterers: 9134 At special positions: 0 Unit cell: (122.451, 89.523, 128.625, 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 65 16.00 O 1652 8.00 N 1510 7.00 C 5907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QXV L 9 " Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'R' and resid 21 through 50 Proline residue: R 29 - end of helix removed outlier: 3.665A pdb=" N VAL R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.705A pdb=" N SER R 73 " --> pdb=" O LEU R 69 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.943A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.702A pdb=" N LYS R 99 " --> pdb=" O TRP R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 157 removed outlier: 4.231A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 164 removed outlier: 4.242A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 186 through 210 removed outlier: 4.237A pdb=" N LYS R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE R 208 " --> pdb=" O ILE R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 removed outlier: 3.712A pdb=" N SER R 215 " --> pdb=" O SER R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 267 removed outlier: 3.707A pdb=" N VAL R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE R 252 " --> pdb=" O ALA R 248 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP R 254 " --> pdb=" O PHE R 250 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE R 255 " --> pdb=" O PHE R 251 " (cutoff:3.500A) Proline residue: R 256 - end of helix removed outlier: 3.595A pdb=" N VAL R 260 " --> pdb=" O PRO R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.646A pdb=" N ILE R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL R 284 " --> pdb=" O ILE R 280 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.583A pdb=" N ASN R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.741A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.705A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 removed outlier: 4.144A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.072A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.521A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.147A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.993A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.647A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 7.108A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.526A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.157A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.979A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.897A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.907A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.536A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.563A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.048A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1236 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: 2.56 Time building geometry restraints manager: 2.95 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: 2798 1.34 - 1.46: 2015 1.46 - 1.58: 4429 1.58 - 1.70: 1 1.70 - 1.82: 96 Bond restraints: 9339 Sorted by residual: bond pdb=" C QXV L 9 " pdb=" NXT QXV L 9 " ideal model delta sigma weight residual 1.339 1.444 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CG LEU B 336 " pdb=" CD2 LEU B 336 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CG LEU B 70 " pdb=" CD2 LEU B 70 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CG LEU B 336 " pdb=" CD1 LEU B 336 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.19e+00 bond pdb=" C LEU R 162 " pdb=" N PHE R 163 " ideal model delta sigma weight residual 1.334 1.369 -0.034 1.43e-02 4.89e+03 5.77e+00 ... (remaining 9334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 11967 1.84 - 3.68: 566 3.68 - 5.52: 91 5.52 - 7.37: 30 7.37 - 9.21: 8 Bond angle restraints: 12662 Sorted by residual: angle pdb=" N VAL R 160 " pdb=" CA VAL R 160 " pdb=" C VAL R 160 " ideal model delta sigma weight residual 110.72 116.43 -5.71 1.01e+00 9.80e-01 3.20e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.35 127.61 -5.26 1.46e+00 4.69e-01 1.30e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.00e+00 1.00e+00 1.21e+01 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 5426 15.10 - 30.20: 247 30.20 - 45.30: 80 45.30 - 60.40: 1 60.40 - 75.50: 4 Dihedral angle restraints: 5758 sinusoidal: 2468 harmonic: 3290 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -121.33 35.33 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CA HIS E 35 " pdb=" C HIS E 35 " pdb=" N TRP E 36 " pdb=" CA TRP E 36 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1298 0.096 - 0.192: 135 0.192 - 0.288: 7 0.288 - 0.384: 6 0.384 - 0.480: 4 Chirality restraints: 1450 Sorted by residual: chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C15 CLR R 404 " pdb=" C8 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1447 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 158 " 0.016 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C LEU R 158 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU R 158 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO R 159 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " 0.018 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP E 111 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 27 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ILE R 27 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE R 27 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU R 28 " 0.013 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 911 2.76 - 3.29: 8556 3.29 - 3.83: 15205 3.83 - 4.36: 17772 4.36 - 4.90: 31044 Nonbonded interactions: 73488 Sorted by model distance: nonbonded pdb=" O ALA R 153 " pdb=" OG1 THR R 157 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS C 44 " model vdw 2.279 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.352 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.357 3.040 ... (remaining 73483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 7.770 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.360 Set scattering table: 0.000 Process input model: 24.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 0.105 9339 Z= 0.328 Angle : 0.928 9.207 12662 Z= 0.483 Chirality : 0.064 0.480 1450 Planarity : 0.006 0.048 1555 Dihedral : 9.848 75.504 3629 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.94 (0.21), residues: 1123 helix: -1.84 (0.20), residues: 410 sheet: -1.61 (0.29), residues: 273 loop : -2.06 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP E 111 HIS 0.008 0.002 HIS E 35 PHE 0.033 0.003 PHE R 161 TYR 0.021 0.002 TYR E 59 ARG 0.015 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 39 LEU cc_start: 0.8789 (tt) cc_final: 0.8500 (tt) REVERT: R 90 LYS cc_start: 0.7884 (mttt) cc_final: 0.6884 (mmmt) REVERT: R 174 THR cc_start: 0.6256 (p) cc_final: 0.5610 (p) REVERT: R 179 ASN cc_start: 0.7691 (t0) cc_final: 0.7161 (m110) REVERT: R 191 LEU cc_start: 0.6671 (tp) cc_final: 0.6432 (pp) REVERT: R 300 MET cc_start: 0.8486 (mtt) cc_final: 0.8215 (mtm) REVERT: A 48 THR cc_start: 0.8560 (m) cc_final: 0.8289 (p) REVERT: A 327 THR cc_start: 0.8168 (p) cc_final: 0.7403 (m) REVERT: A 346 ASN cc_start: 0.8778 (m-40) cc_final: 0.8513 (m110) REVERT: B 267 ASP cc_start: 0.8710 (m-30) cc_final: 0.8263 (t0) REVERT: B 273 ILE cc_start: 0.8378 (mp) cc_final: 0.8163 (mt) REVERT: B 291 ASP cc_start: 0.7792 (t70) cc_final: 0.7490 (t70) REVERT: B 297 TRP cc_start: 0.8763 (m100) cc_final: 0.8362 (m100) REVERT: E 217 SER cc_start: 0.8144 (t) cc_final: 0.6768 (p) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2550 time to fit residues: 108.0648 Evaluate side-chains 203 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 GLN A 204 GLN B 32 GLN B 62 HIS B 91 HIS B 175 GLN E 13 GLN E 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 9339 Z= 0.267 Angle : 0.622 8.237 12662 Z= 0.321 Chirality : 0.043 0.150 1450 Planarity : 0.004 0.036 1555 Dihedral : 6.130 56.219 1596 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.87 % Allowed : 11.99 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.37 (0.23), residues: 1123 helix: 0.11 (0.25), residues: 417 sheet: -1.21 (0.29), residues: 268 loop : -1.59 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.006 0.001 HIS B 91 PHE 0.017 0.001 PHE R 96 TYR 0.016 0.002 TYR B 59 ARG 0.006 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 90 LYS cc_start: 0.8183 (mttt) cc_final: 0.7854 (mmmm) REVERT: R 191 LEU cc_start: 0.7045 (tp) cc_final: 0.6665 (pp) REVERT: R 269 LYS cc_start: 0.8251 (mptt) cc_final: 0.7964 (mtpt) REVERT: R 300 MET cc_start: 0.8755 (mtt) cc_final: 0.8487 (mtm) REVERT: A 48 THR cc_start: 0.8601 (m) cc_final: 0.8373 (p) REVERT: A 52 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: A 315 ASP cc_start: 0.7689 (p0) cc_final: 0.7397 (p0) REVERT: A 327 THR cc_start: 0.7870 (p) cc_final: 0.7496 (m) REVERT: A 331 ASN cc_start: 0.8115 (m-40) cc_final: 0.7849 (m110) REVERT: A 346 ASN cc_start: 0.8869 (m-40) cc_final: 0.8563 (m110) REVERT: B 10 GLU cc_start: 0.8098 (tp30) cc_final: 0.7882 (tp30) REVERT: B 101 MET cc_start: 0.8583 (mmm) cc_final: 0.8382 (mmm) REVERT: B 267 ASP cc_start: 0.8840 (m-30) cc_final: 0.8363 (t0) REVERT: B 273 ILE cc_start: 0.8507 (mp) cc_final: 0.8214 (mt) REVERT: B 291 ASP cc_start: 0.8173 (t70) cc_final: 0.7879 (t70) REVERT: B 297 TRP cc_start: 0.8874 (m100) cc_final: 0.8460 (m100) REVERT: C 13 ARG cc_start: 0.7951 (ptp-110) cc_final: 0.7578 (ttm-80) REVERT: E 6 GLU cc_start: 0.8258 (mp0) cc_final: 0.7771 (mp0) REVERT: E 153 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8149 (pt0) REVERT: E 220 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7794 (mp0) outliers start: 28 outliers final: 12 residues processed: 230 average time/residue: 0.2531 time to fit residues: 78.5291 Evaluate side-chains 197 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 258 GLN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 175 GLN E 13 GLN E 77 ASN E 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 9339 Z= 0.332 Angle : 0.639 9.228 12662 Z= 0.327 Chirality : 0.044 0.205 1450 Planarity : 0.004 0.045 1555 Dihedral : 6.101 58.170 1596 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.79 % Allowed : 13.52 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.24), residues: 1123 helix: 0.76 (0.26), residues: 413 sheet: -0.94 (0.29), residues: 255 loop : -1.33 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.006 0.001 HIS B 91 PHE 0.013 0.002 PHE B 234 TYR 0.018 0.002 TYR B 59 ARG 0.006 0.001 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 183 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 90 LYS cc_start: 0.8259 (mttt) cc_final: 0.7925 (mmmm) REVERT: R 161 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8101 (t80) REVERT: R 191 LEU cc_start: 0.7157 (tp) cc_final: 0.6750 (pp) REVERT: R 271 MET cc_start: 0.8236 (mtp) cc_final: 0.7998 (mtp) REVERT: R 300 MET cc_start: 0.8835 (mtt) cc_final: 0.8487 (mtm) REVERT: A 48 THR cc_start: 0.8651 (m) cc_final: 0.8431 (p) REVERT: A 52 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: A 242 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7469 (mtt90) REVERT: A 331 ASN cc_start: 0.8255 (m-40) cc_final: 0.7942 (m110) REVERT: B 10 GLU cc_start: 0.8113 (tp30) cc_final: 0.7838 (tp30) REVERT: B 267 ASP cc_start: 0.8870 (m-30) cc_final: 0.8377 (t0) REVERT: B 291 ASP cc_start: 0.8322 (t70) cc_final: 0.7994 (t70) REVERT: C 13 ARG cc_start: 0.8174 (ptp-110) cc_final: 0.7752 (ttm-80) outliers start: 37 outliers final: 21 residues processed: 207 average time/residue: 0.2209 time to fit residues: 61.8175 Evaluate side-chains 196 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN E 13 GLN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 9339 Z= 0.297 Angle : 0.631 9.169 12662 Z= 0.318 Chirality : 0.042 0.182 1450 Planarity : 0.004 0.047 1555 Dihedral : 5.919 59.235 1596 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.61 % Allowed : 14.45 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.55 (0.24), residues: 1123 helix: 0.99 (0.26), residues: 417 sheet: -0.81 (0.30), residues: 257 loop : -1.31 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 95 HIS 0.007 0.001 HIS R 102 PHE 0.010 0.001 PHE E 27 TYR 0.013 0.001 TYR B 59 ARG 0.003 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.7178 (ptp-170) REVERT: R 44 ASN cc_start: 0.8336 (m-40) cc_final: 0.7948 (m110) REVERT: R 161 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8170 (t80) REVERT: R 191 LEU cc_start: 0.7220 (tp) cc_final: 0.6807 (pp) REVERT: R 300 MET cc_start: 0.8905 (mtt) cc_final: 0.8581 (mtm) REVERT: A 48 THR cc_start: 0.8626 (m) cc_final: 0.8397 (p) REVERT: A 52 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6653 (tt0) REVERT: A 331 ASN cc_start: 0.8260 (m-40) cc_final: 0.7920 (m110) REVERT: B 10 GLU cc_start: 0.8116 (tp30) cc_final: 0.7842 (tp30) REVERT: B 219 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8418 (mtt-85) REVERT: B 267 ASP cc_start: 0.8888 (m-30) cc_final: 0.8497 (t0) REVERT: B 291 ASP cc_start: 0.8292 (t70) cc_final: 0.7962 (t70) REVERT: C 13 ARG cc_start: 0.8208 (ptp-110) cc_final: 0.7759 (ttm-80) REVERT: C 16 VAL cc_start: 0.9077 (t) cc_final: 0.8715 (m) REVERT: E 161 SER cc_start: 0.8972 (t) cc_final: 0.8611 (t) REVERT: E 218 ARG cc_start: 0.6672 (mmp-170) cc_final: 0.6412 (mmp-170) REVERT: E 220 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7728 (mp0) outliers start: 45 outliers final: 28 residues processed: 208 average time/residue: 0.2239 time to fit residues: 64.3509 Evaluate side-chains 203 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.0270 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 175 GLN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9339 Z= 0.190 Angle : 0.578 9.347 12662 Z= 0.293 Chirality : 0.041 0.147 1450 Planarity : 0.003 0.047 1555 Dihedral : 5.473 56.865 1596 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.20 % Allowed : 15.47 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.32 (0.25), residues: 1123 helix: 1.11 (0.26), residues: 425 sheet: -0.53 (0.31), residues: 251 loop : -1.26 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 95 HIS 0.005 0.001 HIS R 102 PHE 0.012 0.001 PHE R 163 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: R 39 LEU cc_start: 0.9257 (tp) cc_final: 0.8873 (tt) REVERT: R 44 ASN cc_start: 0.8315 (m-40) cc_final: 0.7956 (m110) REVERT: R 157 THR cc_start: 0.8202 (m) cc_final: 0.7851 (t) REVERT: R 161 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8123 (t80) REVERT: R 191 LEU cc_start: 0.7071 (tp) cc_final: 0.6667 (pp) REVERT: R 300 MET cc_start: 0.8907 (mtt) cc_final: 0.8589 (mtm) REVERT: A 48 THR cc_start: 0.8552 (m) cc_final: 0.8311 (p) REVERT: A 52 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: A 242 ARG cc_start: 0.7888 (mtt-85) cc_final: 0.7628 (mtt-85) REVERT: A 306 GLN cc_start: 0.8505 (tp40) cc_final: 0.8258 (tp40) REVERT: A 316 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7527 (t) REVERT: A 331 ASN cc_start: 0.8184 (m-40) cc_final: 0.7839 (m110) REVERT: B 10 GLU cc_start: 0.8100 (tp30) cc_final: 0.7811 (tp30) REVERT: B 172 GLU cc_start: 0.8525 (pm20) cc_final: 0.8091 (pm20) REVERT: B 267 ASP cc_start: 0.8848 (m-30) cc_final: 0.8442 (t0) REVERT: B 291 ASP cc_start: 0.8179 (t70) cc_final: 0.7853 (t70) REVERT: B 297 TRP cc_start: 0.8736 (m100) cc_final: 0.8435 (m100) REVERT: C 13 ARG cc_start: 0.8238 (ptp-110) cc_final: 0.7840 (ttm-80) REVERT: C 16 VAL cc_start: 0.9093 (t) cc_final: 0.8714 (m) REVERT: E 6 GLU cc_start: 0.8249 (mp0) cc_final: 0.7960 (mp0) REVERT: E 140 MET cc_start: 0.9049 (mmm) cc_final: 0.8501 (mmm) REVERT: E 161 SER cc_start: 0.8955 (t) cc_final: 0.8512 (t) REVERT: E 218 ARG cc_start: 0.6747 (mmp-170) cc_final: 0.6511 (mmm160) REVERT: E 219 LEU cc_start: 0.8628 (mt) cc_final: 0.8427 (mt) outliers start: 41 outliers final: 25 residues processed: 209 average time/residue: 0.2181 time to fit residues: 62.7486 Evaluate side-chains 201 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 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 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9339 Z= 0.207 Angle : 0.593 8.580 12662 Z= 0.299 Chirality : 0.041 0.152 1450 Planarity : 0.003 0.048 1555 Dihedral : 5.305 55.225 1596 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.00 % Allowed : 15.88 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1123 helix: 1.18 (0.26), residues: 424 sheet: -0.39 (0.31), residues: 262 loop : -1.23 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 95 HIS 0.005 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.013 0.001 TYR B 59 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7369 (ttp-110) cc_final: 0.7121 (ptp-110) REVERT: R 44 ASN cc_start: 0.8408 (m-40) cc_final: 0.7966 (m110) REVERT: R 157 THR cc_start: 0.8241 (m) cc_final: 0.7906 (t) REVERT: R 161 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8177 (t80) REVERT: R 179 ASN cc_start: 0.7682 (t0) cc_final: 0.6266 (m110) REVERT: R 191 LEU cc_start: 0.6901 (tp) cc_final: 0.6579 (pp) REVERT: R 300 MET cc_start: 0.8898 (mtt) cc_final: 0.8585 (mtm) REVERT: A 48 THR cc_start: 0.8488 (m) cc_final: 0.8239 (p) REVERT: A 52 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6608 (tt0) REVERT: A 242 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7754 (mtt-85) REVERT: A 306 GLN cc_start: 0.8488 (tp40) cc_final: 0.8240 (tp40) REVERT: A 316 THR cc_start: 0.7932 (p) cc_final: 0.7423 (t) REVERT: A 331 ASN cc_start: 0.8217 (m-40) cc_final: 0.7872 (m110) REVERT: B 10 GLU cc_start: 0.8134 (tp30) cc_final: 0.7776 (tp30) REVERT: B 217 MET cc_start: 0.7702 (ppp) cc_final: 0.7451 (ppp) REVERT: B 234 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.9055 (m-80) REVERT: B 243 THR cc_start: 0.8819 (m) cc_final: 0.8548 (p) REVERT: B 267 ASP cc_start: 0.8850 (m-30) cc_final: 0.8435 (t0) REVERT: B 291 ASP cc_start: 0.8176 (t70) cc_final: 0.7877 (t70) REVERT: B 297 TRP cc_start: 0.8724 (m100) cc_final: 0.8448 (m100) REVERT: C 13 ARG cc_start: 0.8185 (ptp-110) cc_final: 0.7793 (ttm-80) REVERT: E 6 GLU cc_start: 0.8250 (mp0) cc_final: 0.8025 (mp0) REVERT: E 140 MET cc_start: 0.9069 (mmm) cc_final: 0.8329 (mmm) REVERT: E 219 LEU cc_start: 0.8630 (mt) cc_final: 0.8417 (mt) outliers start: 39 outliers final: 26 residues processed: 204 average time/residue: 0.2114 time to fit residues: 59.5275 Evaluate side-chains 199 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9339 Z= 0.205 Angle : 0.595 8.524 12662 Z= 0.300 Chirality : 0.041 0.154 1450 Planarity : 0.003 0.048 1555 Dihedral : 5.137 55.160 1596 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.59 % Allowed : 16.39 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.18 (0.25), residues: 1123 helix: 1.21 (0.26), residues: 426 sheet: -0.43 (0.31), residues: 269 loop : -1.21 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 95 HIS 0.005 0.001 HIS R 102 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7335 (ttp-110) cc_final: 0.7131 (ptp-110) REVERT: R 39 LEU cc_start: 0.9176 (tp) cc_final: 0.8831 (tt) REVERT: R 44 ASN cc_start: 0.8411 (m-40) cc_final: 0.7976 (m110) REVERT: R 157 THR cc_start: 0.8220 (m) cc_final: 0.7917 (t) REVERT: R 161 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8236 (t80) REVERT: R 179 ASN cc_start: 0.7856 (t0) cc_final: 0.6344 (m110) REVERT: R 191 LEU cc_start: 0.6898 (tp) cc_final: 0.6581 (pp) REVERT: R 300 MET cc_start: 0.8900 (mtt) cc_final: 0.8582 (mtm) REVERT: A 48 THR cc_start: 0.8367 (m) cc_final: 0.8110 (p) REVERT: A 52 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6664 (tt0) REVERT: A 242 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7789 (mtt-85) REVERT: A 306 GLN cc_start: 0.8481 (tp40) cc_final: 0.8235 (tp40) REVERT: A 316 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7449 (t) REVERT: A 331 ASN cc_start: 0.8230 (m-40) cc_final: 0.7867 (m110) REVERT: B 10 GLU cc_start: 0.8134 (tp30) cc_final: 0.7755 (tp30) REVERT: B 172 GLU cc_start: 0.8404 (pm20) cc_final: 0.8173 (pm20) REVERT: B 234 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.9066 (m-80) REVERT: B 243 THR cc_start: 0.8806 (m) cc_final: 0.8536 (p) REVERT: B 252 LEU cc_start: 0.9176 (tt) cc_final: 0.8943 (tt) REVERT: B 267 ASP cc_start: 0.8842 (m-30) cc_final: 0.8415 (t0) REVERT: B 291 ASP cc_start: 0.8148 (t70) cc_final: 0.7855 (t70) REVERT: B 297 TRP cc_start: 0.8696 (m100) cc_final: 0.8433 (m100) REVERT: C 13 ARG cc_start: 0.8199 (ptp-110) cc_final: 0.7830 (ttm-80) outliers start: 35 outliers final: 24 residues processed: 203 average time/residue: 0.1992 time to fit residues: 56.6613 Evaluate side-chains 203 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9339 Z= 0.197 Angle : 0.588 8.144 12662 Z= 0.298 Chirality : 0.041 0.154 1450 Planarity : 0.003 0.048 1555 Dihedral : 4.992 55.646 1596 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.79 % Allowed : 16.50 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.09 (0.25), residues: 1123 helix: 1.28 (0.26), residues: 425 sheet: -0.38 (0.30), residues: 274 loop : -1.16 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 91 HIS 0.005 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7349 (ttp-110) cc_final: 0.7142 (ptp-110) REVERT: R 39 LEU cc_start: 0.9184 (tp) cc_final: 0.8829 (tt) REVERT: R 44 ASN cc_start: 0.8415 (m-40) cc_final: 0.7981 (m110) REVERT: R 81 LEU cc_start: 0.8646 (mt) cc_final: 0.8438 (mt) REVERT: R 157 THR cc_start: 0.8280 (m) cc_final: 0.7996 (t) REVERT: R 179 ASN cc_start: 0.7882 (t0) cc_final: 0.6439 (m110) REVERT: R 191 LEU cc_start: 0.6925 (tp) cc_final: 0.6649 (pp) REVERT: R 300 MET cc_start: 0.8898 (mtt) cc_final: 0.8580 (mtm) REVERT: A 48 THR cc_start: 0.8238 (m) cc_final: 0.7978 (p) REVERT: A 52 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6774 (tt0) REVERT: A 242 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7788 (mtt-85) REVERT: A 316 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7365 (t) REVERT: A 331 ASN cc_start: 0.8253 (m-40) cc_final: 0.7916 (m110) REVERT: B 10 GLU cc_start: 0.8148 (tp30) cc_final: 0.7924 (tp30) REVERT: B 155 ASN cc_start: 0.8164 (t0) cc_final: 0.7961 (t0) REVERT: B 207 SER cc_start: 0.8687 (m) cc_final: 0.8465 (p) REVERT: B 217 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7405 (ppp) REVERT: B 234 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8993 (m-80) REVERT: B 243 THR cc_start: 0.8849 (m) cc_final: 0.8551 (p) REVERT: B 267 ASP cc_start: 0.8814 (m-30) cc_final: 0.8372 (t0) REVERT: B 291 ASP cc_start: 0.8146 (t70) cc_final: 0.7870 (t70) REVERT: B 297 TRP cc_start: 0.8677 (m100) cc_final: 0.8471 (m100) REVERT: C 13 ARG cc_start: 0.8235 (ptp-110) cc_final: 0.7832 (ttm-80) outliers start: 37 outliers final: 25 residues processed: 209 average time/residue: 0.2043 time to fit residues: 59.4494 Evaluate side-chains 209 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN A 204 GLN E 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9339 Z= 0.230 Angle : 0.608 8.313 12662 Z= 0.308 Chirality : 0.041 0.158 1450 Planarity : 0.004 0.049 1555 Dihedral : 5.006 56.174 1596 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.38 % Allowed : 17.73 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.09 (0.25), residues: 1123 helix: 1.32 (0.26), residues: 419 sheet: -0.39 (0.30), residues: 284 loop : -1.17 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 91 HIS 0.005 0.001 HIS R 102 PHE 0.009 0.001 PHE E 27 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7395 (ttp-110) cc_final: 0.7131 (ptp-110) REVERT: R 39 LEU cc_start: 0.9211 (tp) cc_final: 0.8832 (tt) REVERT: R 81 LEU cc_start: 0.8648 (mt) cc_final: 0.8448 (mt) REVERT: R 157 THR cc_start: 0.8373 (m) cc_final: 0.8047 (t) REVERT: R 179 ASN cc_start: 0.7925 (t0) cc_final: 0.6450 (m110) REVERT: R 191 LEU cc_start: 0.6942 (tp) cc_final: 0.6673 (pp) REVERT: R 293 PHE cc_start: 0.8539 (t80) cc_final: 0.8189 (t80) REVERT: R 300 MET cc_start: 0.8910 (mtt) cc_final: 0.8590 (mtm) REVERT: A 48 THR cc_start: 0.8171 (m) cc_final: 0.7904 (p) REVERT: A 52 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6827 (tt0) REVERT: A 242 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7793 (mtt-85) REVERT: A 316 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7405 (t) REVERT: A 331 ASN cc_start: 0.8375 (m-40) cc_final: 0.8068 (m-40) REVERT: B 10 GLU cc_start: 0.8266 (tp30) cc_final: 0.7969 (tp30) REVERT: B 15 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8047 (mtmm) REVERT: B 207 SER cc_start: 0.8658 (m) cc_final: 0.8453 (p) REVERT: B 217 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7428 (ppp) REVERT: B 234 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8956 (m-80) REVERT: B 243 THR cc_start: 0.8836 (m) cc_final: 0.8507 (p) REVERT: B 267 ASP cc_start: 0.8746 (m-30) cc_final: 0.8452 (m-30) REVERT: B 291 ASP cc_start: 0.8179 (t70) cc_final: 0.7924 (t70) REVERT: B 297 TRP cc_start: 0.8708 (m100) cc_final: 0.8480 (m100) REVERT: C 13 ARG cc_start: 0.8277 (ptp-110) cc_final: 0.7892 (ttm-80) REVERT: E 140 MET cc_start: 0.9084 (mmm) cc_final: 0.8829 (mmm) outliers start: 33 outliers final: 26 residues processed: 196 average time/residue: 0.2094 time to fit residues: 57.4661 Evaluate side-chains 201 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 30.0000 chunk 73 optimal weight: 0.0770 chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN A 294 ASN E 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9339 Z= 0.191 Angle : 0.592 8.238 12662 Z= 0.301 Chirality : 0.041 0.197 1450 Planarity : 0.003 0.049 1555 Dihedral : 4.888 55.974 1596 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.38 % Allowed : 18.65 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.02 (0.25), residues: 1123 helix: 1.35 (0.26), residues: 421 sheet: -0.33 (0.30), residues: 279 loop : -1.12 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 PHE 0.011 0.001 PHE B 234 TYR 0.011 0.001 TYR E 190 ARG 0.012 0.000 ARG E 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7379 (ttp-110) cc_final: 0.7111 (ptp-110) REVERT: R 39 LEU cc_start: 0.9196 (tp) cc_final: 0.8865 (tt) REVERT: R 157 THR cc_start: 0.8375 (m) cc_final: 0.8057 (t) REVERT: R 179 ASN cc_start: 0.7872 (t0) cc_final: 0.6401 (m110) REVERT: R 191 LEU cc_start: 0.6932 (tp) cc_final: 0.6676 (pp) REVERT: R 300 MET cc_start: 0.8840 (mtt) cc_final: 0.8510 (mtm) REVERT: A 48 THR cc_start: 0.8023 (m) cc_final: 0.7764 (p) REVERT: A 52 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: A 242 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7801 (mtt-85) REVERT: A 316 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7444 (t) REVERT: A 331 ASN cc_start: 0.8258 (m-40) cc_final: 0.7893 (m110) REVERT: B 10 GLU cc_start: 0.8301 (tp30) cc_final: 0.7890 (tp30) REVERT: B 13 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 15 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8043 (mtmm) REVERT: B 207 SER cc_start: 0.8680 (m) cc_final: 0.8468 (p) REVERT: B 217 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7359 (ppp) REVERT: B 243 THR cc_start: 0.8830 (m) cc_final: 0.8507 (p) REVERT: B 267 ASP cc_start: 0.8773 (m-30) cc_final: 0.8449 (m-30) REVERT: B 291 ASP cc_start: 0.8133 (t70) cc_final: 0.7879 (t70) REVERT: B 297 TRP cc_start: 0.8669 (m100) cc_final: 0.8464 (m100) REVERT: C 13 ARG cc_start: 0.8244 (ptp-110) cc_final: 0.7878 (ttm-80) REVERT: E 140 MET cc_start: 0.9073 (mmm) cc_final: 0.8745 (mmm) outliers start: 33 outliers final: 24 residues processed: 197 average time/residue: 0.2103 time to fit residues: 57.0895 Evaluate side-chains 195 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 0.0270 chunk 16 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105972 restraints weight = 13088.894| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.42 r_work: 0.3188 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9339 Z= 0.186 Angle : 0.597 8.592 12662 Z= 0.302 Chirality : 0.041 0.164 1450 Planarity : 0.003 0.049 1555 Dihedral : 4.825 56.601 1596 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.77 % Allowed : 19.26 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.00 (0.25), residues: 1123 helix: 1.34 (0.26), residues: 423 sheet: -0.27 (0.31), residues: 279 loop : -1.13 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 PHE 0.010 0.001 PHE B 234 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2553.85 seconds wall clock time: 49 minutes 3.38 seconds (2943.38 seconds total)