Starting phenix.real_space_refine on Fri Apr 5 23:38:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/04_2024/8gdz_29951_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/04_2024/8gdz_29951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/04_2024/8gdz_29951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/04_2024/8gdz_29951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/04_2024/8gdz_29951_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdz_29951/04_2024/8gdz_29951_updated.pdb" } resolution = 3.5 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= -0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4079 2.51 5 N 1102 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6320 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1644 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 353 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2308 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 170 Chain: "G" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 336 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2017 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 145 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.90, per 1000 atoms: 0.62 Number of scatterers: 6320 At special positions: 0 Unit cell: (68.9, 97.52, 129.32, 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 37 16.00 O 1102 8.00 N 1102 7.00 C 4079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 9 sheets defined 44.9% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.587A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.560A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.990A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'G' and resid 11 through 22 removed outlier: 3.748A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.777A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 60 Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.274A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.503A pdb=" N SER R 161 " --> pdb=" O VAL R 157 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 removed outlier: 4.037A pdb=" N ALA R 186 " --> pdb=" O ILE R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 237 removed outlier: 5.059A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.930A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 305 through 326 removed outlier: 4.217A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 339 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.805A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.595A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.678A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.728A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.289A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.529A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.028A 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: 7.194A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.573A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.063A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 78 through 83 removed outlier: 3.586A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 2.58 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: 2051 1.34 - 1.46: 1604 1.46 - 1.58: 2753 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 6458 Sorted by residual: bond pdb=" CA ARG A 231 " pdb=" C ARG A 231 " ideal model delta sigma weight residual 1.524 1.460 0.063 1.26e-02 6.30e+03 2.51e+01 bond pdb=" CA ARG A 232 " pdb=" C ARG A 232 " ideal model delta sigma weight residual 1.521 1.463 0.058 1.17e-02 7.31e+03 2.50e+01 bond pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta sigma weight residual 1.458 1.415 0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.438 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 6453 not shown) Histogram of bond angle deviations from ideal: 98.93 - 105.96: 88 105.96 - 112.98: 3547 112.98 - 120.01: 2092 120.01 - 127.03: 3053 127.03 - 134.06: 76 Bond angle restraints: 8856 Sorted by residual: angle pdb=" N ARG A 231 " pdb=" CA ARG A 231 " pdb=" C ARG A 231 " ideal model delta sigma weight residual 110.23 99.66 10.57 1.45e+00 4.76e-01 5.32e+01 angle pdb=" C ARG A 232 " pdb=" N LYS A 233 " pdb=" CA LYS A 233 " ideal model delta sigma weight residual 122.54 116.22 6.32 1.65e+00 3.67e-01 1.47e+01 angle pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta sigma weight residual 123.00 117.91 5.09 1.41e+00 5.03e-01 1.30e+01 angle pdb=" CA LEU G 15 " pdb=" CB LEU G 15 " pdb=" CG LEU G 15 " ideal model delta sigma weight residual 116.30 124.07 -7.77 3.50e+00 8.16e-02 4.93e+00 angle pdb=" N GLU B 226 " pdb=" CA GLU B 226 " pdb=" C GLU B 226 " ideal model delta sigma weight residual 113.88 111.24 2.64 1.23e+00 6.61e-01 4.59e+00 ... (remaining 8851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3425 17.69 - 35.37: 224 35.37 - 53.06: 39 53.06 - 70.75: 8 70.75 - 88.43: 4 Dihedral angle restraints: 3700 sinusoidal: 1063 harmonic: 2637 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual -86.00 2.43 -88.43 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" C ARG A 231 " pdb=" N ARG A 231 " pdb=" CA ARG A 231 " pdb=" CB ARG A 231 " ideal model delta harmonic sigma weight residual -122.60 -114.16 -8.44 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CG ARG A 385 " pdb=" CD ARG A 385 " pdb=" NE ARG A 385 " pdb=" CZ ARG A 385 " ideal model delta sinusoidal sigma weight residual -180.00 -136.01 -43.99 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 3697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 692 0.032 - 0.063: 264 0.063 - 0.095: 80 0.095 - 0.126: 33 0.126 - 0.158: 3 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1069 not shown) Planarity restraints: 1121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO G 49 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 236 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ILE R 205 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.008 2.00e-02 2.50e+03 ... (remaining 1118 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1636 2.80 - 3.32: 6164 3.32 - 3.85: 10533 3.85 - 4.37: 11357 4.37 - 4.90: 20580 Nonbonded interactions: 50270 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.280 2.440 nonbonded pdb=" O ALA R 119 " pdb=" OG1 THR R 123 " model vdw 2.285 2.440 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.351 2.440 nonbonded pdb=" OD2 ASP B 212 " pdb=" NH2 ARG B 219 " model vdw 2.363 2.520 ... (remaining 50265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 5.930 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.130 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.003 0.063 6458 Z= 0.243 Angle : 0.509 10.574 8856 Z= 0.277 Chirality : 0.039 0.158 1072 Planarity : 0.003 0.044 1121 Dihedral : 12.959 86.708 1980 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 1.42 (0.28), residues: 886 helix: 2.52 (0.27), residues: 381 sheet: -0.14 (0.38), residues: 175 loop : -0.29 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.004 0.001 HIS R 93 PHE 0.011 0.001 PHE A 222 TYR 0.016 0.001 TYR B 59 ARG 0.006 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.734 Fit side-chains REVERT: B 249 THR cc_start: 0.9229 (p) cc_final: 0.8761 (p) REVERT: B 297 TRP cc_start: 0.8742 (m100) cc_final: 0.8335 (m100) REVERT: R 203 SER cc_start: 0.9392 (t) cc_final: 0.9164 (t) REVERT: R 227 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8402 (mtpt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1667 time to fit residues: 26.6117 Evaluate side-chains 94 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 93 HIS R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6458 Z= 0.191 Angle : 0.459 6.920 8856 Z= 0.245 Chirality : 0.039 0.124 1072 Planarity : 0.003 0.042 1121 Dihedral : 3.884 16.583 969 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.55 % Allowed : 11.22 % Favored : 87.23 % 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: 1.43 (0.28), residues: 886 helix: 2.54 (0.27), residues: 384 sheet: -0.10 (0.38), residues: 167 loop : -0.36 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 PHE 0.011 0.001 PHE A 222 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.712 Fit side-chains REVERT: R 227 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8444 (mtpt) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.1399 time to fit residues: 19.0950 Evaluate side-chains 83 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 225 HIS B 340 ASN R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6458 Z= 0.156 Angle : 0.428 5.739 8856 Z= 0.230 Chirality : 0.039 0.125 1072 Planarity : 0.003 0.039 1121 Dihedral : 3.766 16.054 969 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.13 % Allowed : 13.73 % Favored : 84.14 % 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: 1.41 (0.28), residues: 886 helix: 2.55 (0.27), residues: 383 sheet: -0.20 (0.38), residues: 170 loop : -0.34 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE A 212 TYR 0.011 0.001 TYR R 199 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.729 Fit side-chains REVERT: B 331 SER cc_start: 0.9247 (p) cc_final: 0.9046 (p) REVERT: R 227 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8443 (mtpt) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 0.1484 time to fit residues: 20.0120 Evaluate side-chains 89 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 207 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.0370 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 chunk 23 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 225 HIS B 340 ASN R 93 HIS R 178 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6458 Z= 0.129 Angle : 0.423 7.640 8856 Z= 0.222 Chirality : 0.038 0.126 1072 Planarity : 0.003 0.038 1121 Dihedral : 3.644 17.152 969 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.13 % Allowed : 15.67 % Favored : 82.21 % 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: 1.44 (0.28), residues: 886 helix: 2.58 (0.27), residues: 383 sheet: -0.14 (0.39), residues: 170 loop : -0.34 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS R 93 PHE 0.008 0.001 PHE A 212 TYR 0.010 0.001 TYR R 199 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.741 Fit side-chains REVERT: R 122 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8421 (mm-30) REVERT: R 227 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8430 (mtpt) outliers start: 11 outliers final: 8 residues processed: 97 average time/residue: 0.1506 time to fit residues: 20.6402 Evaluate side-chains 93 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 340 ASN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6458 Z= 0.168 Angle : 0.429 7.271 8856 Z= 0.227 Chirality : 0.039 0.127 1072 Planarity : 0.003 0.038 1121 Dihedral : 3.670 17.607 969 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.90 % Allowed : 17.41 % Favored : 79.69 % 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: 1.45 (0.29), residues: 886 helix: 2.58 (0.27), residues: 382 sheet: -0.14 (0.40), residues: 170 loop : -0.31 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS B 225 PHE 0.014 0.001 PHE R 104 TYR 0.011 0.001 TYR R 199 ARG 0.005 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.736 Fit side-chains REVERT: R 122 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8386 (mm-30) REVERT: R 227 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8463 (mtpt) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.1623 time to fit residues: 22.4576 Evaluate side-chains 97 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 340 ASN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6458 Z= 0.162 Angle : 0.425 7.278 8856 Z= 0.226 Chirality : 0.039 0.128 1072 Planarity : 0.003 0.037 1121 Dihedral : 3.667 17.765 969 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.90 % Allowed : 18.18 % Favored : 78.92 % 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: 1.46 (0.29), residues: 886 helix: 2.57 (0.27), residues: 382 sheet: -0.09 (0.40), residues: 170 loop : -0.32 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.009 0.001 PHE B 292 TYR 0.011 0.001 TYR R 199 ARG 0.007 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.691 Fit side-chains REVERT: R 122 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8404 (mm-30) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.1256 time to fit residues: 18.0820 Evaluate side-chains 95 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.0030 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 340 ASN R 93 HIS R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6458 Z= 0.159 Angle : 0.429 7.438 8856 Z= 0.228 Chirality : 0.039 0.127 1072 Planarity : 0.003 0.037 1121 Dihedral : 3.652 17.765 969 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.06 % Allowed : 17.60 % Favored : 78.34 % 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: 1.48 (0.29), residues: 886 helix: 2.57 (0.27), residues: 381 sheet: -0.06 (0.39), residues: 171 loop : -0.29 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS R 93 PHE 0.008 0.001 PHE A 212 TYR 0.010 0.001 TYR R 199 ARG 0.006 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.832 Fit side-chains REVERT: R 122 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8437 (mm-30) REVERT: R 227 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8412 (mtpt) outliers start: 21 outliers final: 15 residues processed: 98 average time/residue: 0.1286 time to fit residues: 18.8136 Evaluate side-chains 99 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 340 ASN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6458 Z= 0.166 Angle : 0.431 7.350 8856 Z= 0.229 Chirality : 0.039 0.127 1072 Planarity : 0.003 0.036 1121 Dihedral : 3.656 17.723 969 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.87 % Allowed : 17.99 % Favored : 78.14 % 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: 1.48 (0.29), residues: 886 helix: 2.56 (0.27), residues: 381 sheet: -0.10 (0.38), residues: 176 loop : -0.26 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.009 0.001 PHE A 212 TYR 0.011 0.001 TYR R 199 ARG 0.005 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.764 Fit side-chains REVERT: R 227 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8436 (mtpt) outliers start: 20 outliers final: 16 residues processed: 103 average time/residue: 0.1419 time to fit residues: 21.1840 Evaluate side-chains 100 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 0.0770 chunk 75 optimal weight: 0.0870 chunk 79 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 340 ASN R 93 HIS R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6458 Z= 0.129 Angle : 0.425 7.809 8856 Z= 0.226 Chirality : 0.038 0.127 1072 Planarity : 0.003 0.036 1121 Dihedral : 3.531 17.593 969 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.29 % Allowed : 18.76 % Favored : 77.95 % 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: 1.58 (0.29), residues: 886 helix: 2.67 (0.27), residues: 376 sheet: 0.24 (0.39), residues: 173 loop : -0.38 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS R 93 PHE 0.008 0.001 PHE A 212 TYR 0.010 0.001 TYR A 253 ARG 0.005 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.718 Fit side-chains REVERT: B 259 GLN cc_start: 0.8691 (pt0) cc_final: 0.8479 (pt0) REVERT: R 122 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8415 (mm-30) REVERT: R 227 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8372 (mtpt) outliers start: 17 outliers final: 10 residues processed: 104 average time/residue: 0.1502 time to fit residues: 22.5720 Evaluate side-chains 98 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 56 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 230 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6458 Z= 0.151 Angle : 0.440 9.091 8856 Z= 0.231 Chirality : 0.039 0.126 1072 Planarity : 0.003 0.036 1121 Dihedral : 3.583 17.313 969 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.32 % Allowed : 20.89 % Favored : 76.79 % 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: 1.64 (0.29), residues: 886 helix: 2.58 (0.27), residues: 383 sheet: 0.40 (0.39), residues: 178 loop : -0.30 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE A 212 TYR 0.010 0.001 TYR R 199 ARG 0.005 0.000 ARG R 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.797 Fit side-chains REVERT: A 233 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8252 (ttpp) REVERT: B 226 GLU cc_start: 0.8280 (pm20) cc_final: 0.7994 (pm20) REVERT: R 122 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8418 (mm-30) REVERT: R 227 LYS cc_start: 0.8656 (mtpp) cc_final: 0.8409 (mtpt) outliers start: 12 outliers final: 9 residues processed: 96 average time/residue: 0.1429 time to fit residues: 19.9535 Evaluate side-chains 93 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.0870 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 340 ASN R 93 HIS R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096758 restraints weight = 12874.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099626 restraints weight = 6097.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101586 restraints weight = 3714.968| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6458 Z= 0.160 Angle : 0.448 9.529 8856 Z= 0.236 Chirality : 0.039 0.127 1072 Planarity : 0.003 0.036 1121 Dihedral : 3.632 17.296 969 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.71 % Allowed : 21.28 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.29), residues: 886 helix: 2.63 (0.27), residues: 382 sheet: 0.28 (0.39), residues: 184 loop : -0.31 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 93 PHE 0.008 0.001 PHE A 212 TYR 0.010 0.001 TYR R 199 ARG 0.005 0.000 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1519.01 seconds wall clock time: 28 minutes 32.53 seconds (1712.53 seconds total)