Starting phenix.real_space_refine on Thu Jan 18 14:13:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j18_35913/01_2024/8j18_35913_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j18_35913/01_2024/8j18_35913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j18_35913/01_2024/8j18_35913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j18_35913/01_2024/8j18_35913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j18_35913/01_2024/8j18_35913_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j18_35913/01_2024/8j18_35913_updated.pdb" } resolution = 2.89 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= 0.006 sd= 0.062 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 59 5.16 5 C 5652 2.51 5 N 1528 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R ARG 203": "NH1" <-> "NH2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1759 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Chain: "S" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'HXD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.08, per 1000 atoms: 0.57 Number of scatterers: 8860 At special positions: 0 Unit cell: (109.5, 109.5, 121.91, 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 59 16.00 O 1621 8.00 N 1528 7.00 C 5652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 166 " distance=2.03 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 34.6% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.536A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.827A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 350 removed outlier: 4.261A pdb=" N VAL A 332 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 339 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 344 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 348 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.631A pdb=" N LEU G 15 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU G 17 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS G 20 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 20 through 47 Processing helix chain 'R' and resid 49 through 51 No H-bonds generated for 'chain 'R' and resid 49 through 51' Processing helix chain 'R' and resid 56 through 78 removed outlier: 3.967A pdb=" N GLN R 74 " --> pdb=" O CYS R 70 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 90 through 123 removed outlier: 4.160A pdb=" N ARG R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 131 Proline residue: R 129 - end of helix No H-bonds generated for 'chain 'R' and resid 125 through 131' Processing helix chain 'R' and resid 134 through 158 removed outlier: 3.756A pdb=" N VAL R 138 " --> pdb=" O ALA R 134 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Proline residue: R 154 - end of helix Proline residue: R 157 - end of helix Processing helix chain 'R' and resid 176 through 215 removed outlier: 3.674A pdb=" N GLN R 214 " --> pdb=" O GLN R 210 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR R 215 " --> pdb=" O ALA R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 341 Proline residue: R 334 - end of helix Processing helix chain 'R' and resid 351 through 369 removed outlier: 3.616A pdb=" N TRP R 360 " --> pdb=" O ALA R 356 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU R 361 " --> pdb=" O ASN R 357 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY R 363 " --> pdb=" O THR R 359 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS R 364 " --> pdb=" O TRP R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 375 through 387 Processing helix chain 'R' and resid 389 through 393 removed outlier: 3.566A pdb=" N HIS R 393 " --> pdb=" O ARG R 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.311A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.724A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.983A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.786A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.645A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.687A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.616A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.778A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 159 through 162 removed outlier: 3.944A pdb=" N THR R 167 " --> pdb=" O VAL R 162 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.778A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= M, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.213A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1083 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: 2.90 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1412 1.29 - 1.42: 2409 1.42 - 1.55: 5131 1.55 - 1.68: 9 1.68 - 1.81: 82 Bond restraints: 9043 Sorted by residual: bond pdb=" C THR R 35 " pdb=" O THR R 35 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.16e-02 7.43e+03 4.11e+01 bond pdb=" C ASN B 313 " pdb=" O ASN B 313 " ideal model delta sigma weight residual 1.234 1.159 0.075 1.28e-02 6.10e+03 3.44e+01 bond pdb=" C ASP B 228 " pdb=" O ASP B 228 " ideal model delta sigma weight residual 1.234 1.177 0.057 1.21e-02 6.83e+03 2.25e+01 bond pdb=" C ARG R 176 " pdb=" O ARG R 176 " ideal model delta sigma weight residual 1.238 1.196 0.042 9.50e-03 1.11e+04 1.98e+01 bond pdb=" C ILE S 157 " pdb=" O ILE S 157 " ideal model delta sigma weight residual 1.236 1.193 0.044 9.90e-03 1.02e+04 1.93e+01 ... (remaining 9038 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.29: 195 106.29 - 113.22: 4886 113.22 - 120.15: 3234 120.15 - 127.08: 3838 127.08 - 134.01: 97 Bond angle restraints: 12250 Sorted by residual: angle pdb=" CA THR R 35 " pdb=" C THR R 35 " pdb=" O THR R 35 " ideal model delta sigma weight residual 120.90 114.94 5.96 1.03e+00 9.43e-01 3.35e+01 angle pdb=" N VAL R 78 " pdb=" CA VAL R 78 " pdb=" C VAL R 78 " ideal model delta sigma weight residual 110.72 105.40 5.32 1.01e+00 9.80e-01 2.78e+01 angle pdb=" CA THR R 35 " pdb=" C THR R 35 " pdb=" N VAL R 36 " ideal model delta sigma weight residual 117.02 123.00 -5.98 1.17e+00 7.31e-01 2.62e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 111.56 105.01 6.55 1.38e+00 5.25e-01 2.25e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 110.24 116.34 -6.10 1.30e+00 5.92e-01 2.20e+01 ... (remaining 12245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4718 17.35 - 34.70: 468 34.70 - 52.05: 128 52.05 - 69.39: 33 69.39 - 86.74: 13 Dihedral angle restraints: 5360 sinusoidal: 2070 harmonic: 3290 Sorted by residual: dihedral pdb=" CA VAL R 78 " pdb=" C VAL R 78 " pdb=" N ASP R 79 " pdb=" CA ASP R 79 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1235 0.065 - 0.130: 145 0.130 - 0.195: 15 0.195 - 0.260: 4 0.260 - 0.325: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA THR R 35 " pdb=" N THR R 35 " pdb=" C THR R 35 " pdb=" CB THR R 35 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA ARG R 176 " pdb=" N ARG R 176 " pdb=" C ARG R 176 " pdb=" CB ARG R 176 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA TYR R 332 " pdb=" N TYR R 332 " pdb=" C TYR R 332 " pdb=" CB TYR R 332 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1397 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 312 " -0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ASP B 312 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP B 312 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN B 313 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 175 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C GLY R 175 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY R 175 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG R 176 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 247 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C ASP B 247 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP B 247 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA B 248 " -0.016 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 493 2.72 - 3.27: 9395 3.27 - 3.81: 14688 3.81 - 4.36: 18560 4.36 - 4.90: 32241 Nonbonded interactions: 75377 Sorted by model distance: nonbonded pdb=" O ASP R 79 " pdb=" OG1 THR R 80 " model vdw 2.181 2.440 nonbonded pdb=" O ASP B 163 " pdb=" CG2 THR B 164 " model vdw 2.269 3.460 nonbonded pdb=" OG1 THR B 164 " pdb=" O HIS B 183 " model vdw 2.280 2.440 nonbonded pdb=" O LYS G 32 " pdb=" OD1 ASP G 36 " model vdw 2.301 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.303 2.440 ... (remaining 75372 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 3.940 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.260 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.004 0.075 9043 Z= 0.276 Angle : 0.707 6.765 12250 Z= 0.430 Chirality : 0.045 0.325 1400 Planarity : 0.004 0.052 1544 Dihedral : 15.965 86.742 3234 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.26 % Allowed : 20.15 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1119 helix: 0.95 (0.29), residues: 370 sheet: -0.45 (0.29), residues: 290 loop : -0.67 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 83 PHE 0.009 0.001 PHE R 152 TYR 0.041 0.002 TYR S 59 ARG 0.007 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8275 (mt) cc_final: 0.7683 (tp) REVERT: B 124 TYR cc_start: 0.9060 (m-80) cc_final: 0.8703 (m-80) REVERT: B 188 MET cc_start: 0.8746 (mmm) cc_final: 0.8331 (mmm) REVERT: B 189 SER cc_start: 0.8703 (t) cc_final: 0.8260 (t) REVERT: B 217 MET cc_start: 0.8116 (tpp) cc_final: 0.7897 (tpt) REVERT: B 237 ASN cc_start: 0.8259 (t0) cc_final: 0.7993 (t0) REVERT: B 259 GLN cc_start: 0.7583 (pt0) cc_final: 0.7085 (pt0) REVERT: G 62 ARG cc_start: 0.7203 (ttm110) cc_final: 0.6820 (ttm110) REVERT: R 81 TYR cc_start: 0.8313 (m-80) cc_final: 0.7856 (m-80) REVERT: R 170 PHE cc_start: 0.8046 (p90) cc_final: 0.7081 (p90) REVERT: R 171 ASP cc_start: 0.8440 (t0) cc_final: 0.7953 (t0) REVERT: S 3 GLN cc_start: 0.7756 (tt0) cc_final: 0.7260 (pt0) REVERT: S 218 ARG cc_start: 0.6257 (ptp-170) cc_final: 0.6011 (ptp90) outliers start: 12 outliers final: 2 residues processed: 182 average time/residue: 1.3080 time to fit residues: 252.4744 Evaluate side-chains 149 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 390 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.2980 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 GLN R 83 HIS R 202 HIS ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 339 ASN ** R 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN S 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9043 Z= 0.214 Angle : 0.574 7.698 12250 Z= 0.300 Chirality : 0.044 0.210 1400 Planarity : 0.004 0.036 1544 Dihedral : 5.722 49.290 1252 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.36 % Allowed : 20.15 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1119 helix: 1.15 (0.27), residues: 375 sheet: -0.19 (0.30), residues: 287 loop : -0.43 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 83 PHE 0.022 0.001 PHE B 253 TYR 0.015 0.001 TYR B 59 ARG 0.006 0.001 ARG R 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8382 (mt) cc_final: 0.7852 (tp) REVERT: B 188 MET cc_start: 0.8630 (mmm) cc_final: 0.8268 (mmm) REVERT: B 189 SER cc_start: 0.8823 (t) cc_final: 0.8426 (t) REVERT: B 217 MET cc_start: 0.8220 (tpp) cc_final: 0.7936 (tpt) REVERT: B 259 GLN cc_start: 0.7649 (pt0) cc_final: 0.7037 (pt0) REVERT: B 270 ILE cc_start: 0.9132 (tt) cc_final: 0.8898 (pp) REVERT: G 52 THR cc_start: 0.7462 (t) cc_final: 0.7113 (p) REVERT: G 58 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8010 (mp0) REVERT: G 62 ARG cc_start: 0.7134 (ttm110) cc_final: 0.6929 (ttm110) REVERT: R 74 GLN cc_start: 0.8895 (tp40) cc_final: 0.8608 (tp-100) REVERT: R 170 PHE cc_start: 0.7980 (p90) cc_final: 0.7162 (p90) REVERT: R 171 ASP cc_start: 0.8369 (t0) cc_final: 0.7810 (t0) REVERT: R 327 CYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7726 (t) REVERT: S 3 GLN cc_start: 0.7590 (tt0) cc_final: 0.7190 (pt0) REVERT: S 20 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8236 (mt) REVERT: S 39 GLN cc_start: 0.8071 (tt0) cc_final: 0.7576 (tt0) REVERT: S 233 LEU cc_start: 0.8206 (tp) cc_final: 0.7852 (mt) outliers start: 32 outliers final: 10 residues processed: 180 average time/residue: 1.1495 time to fit residues: 221.0616 Evaluate side-chains 154 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.0570 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.2700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 239 ASN R 204 GLN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9043 Z= 0.203 Angle : 0.563 8.732 12250 Z= 0.289 Chirality : 0.043 0.186 1400 Planarity : 0.003 0.030 1544 Dihedral : 5.363 46.104 1252 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.51 % Allowed : 20.46 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1119 helix: 1.21 (0.28), residues: 374 sheet: -0.07 (0.30), residues: 287 loop : -0.38 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 83 PHE 0.017 0.001 PHE B 253 TYR 0.018 0.001 TYR B 59 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8430 (mt) cc_final: 0.7922 (tp) REVERT: B 188 MET cc_start: 0.8584 (mmm) cc_final: 0.8246 (mmm) REVERT: B 189 SER cc_start: 0.8847 (t) cc_final: 0.8476 (t) REVERT: B 259 GLN cc_start: 0.7592 (pt0) cc_final: 0.7002 (pt0) REVERT: G 52 THR cc_start: 0.7608 (t) cc_final: 0.7355 (p) REVERT: R 74 GLN cc_start: 0.8735 (tp40) cc_final: 0.8467 (tp-100) REVERT: R 87 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5467 (ttt-90) REVERT: R 170 PHE cc_start: 0.7948 (p90) cc_final: 0.7079 (p90) REVERT: R 171 ASP cc_start: 0.8308 (t0) cc_final: 0.7714 (t0) REVERT: R 327 CYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7668 (t) REVERT: S 3 GLN cc_start: 0.7602 (tt0) cc_final: 0.7174 (pt0) REVERT: S 39 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7433 (tp40) REVERT: S 83 MET cc_start: 0.7788 (mtm) cc_final: 0.7518 (mpp) REVERT: S 179 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7239 (tm-30) REVERT: S 233 LEU cc_start: 0.8213 (tp) cc_final: 0.7858 (mt) REVERT: S 244 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6906 (tmmt) outliers start: 43 outliers final: 15 residues processed: 190 average time/residue: 1.2133 time to fit residues: 247.4659 Evaluate side-chains 167 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 365 ILE Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN R 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9043 Z= 0.160 Angle : 0.539 7.298 12250 Z= 0.275 Chirality : 0.042 0.174 1400 Planarity : 0.003 0.035 1544 Dihedral : 5.000 50.467 1252 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.94 % Allowed : 23.92 % Favored : 73.14 % 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: 0.46 (0.26), residues: 1119 helix: 1.42 (0.28), residues: 368 sheet: 0.02 (0.30), residues: 285 loop : -0.31 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS R 83 PHE 0.015 0.001 PHE B 253 TYR 0.022 0.001 TYR B 59 ARG 0.008 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8463 (mt) cc_final: 0.7979 (tp) REVERT: B 188 MET cc_start: 0.8529 (mmm) cc_final: 0.8209 (mmm) REVERT: B 189 SER cc_start: 0.8780 (t) cc_final: 0.8414 (t) REVERT: B 217 MET cc_start: 0.8182 (tpp) cc_final: 0.7888 (tpt) REVERT: B 259 GLN cc_start: 0.7632 (pt0) cc_final: 0.6948 (pt0) REVERT: B 261 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 262 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7373 (ttp) REVERT: R 87 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.5598 (ttt-90) REVERT: R 106 VAL cc_start: 0.8219 (t) cc_final: 0.7951 (m) REVERT: R 170 PHE cc_start: 0.7930 (p90) cc_final: 0.7086 (p90) REVERT: R 327 CYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7584 (t) REVERT: R 337 LEU cc_start: 0.8118 (mm) cc_final: 0.7910 (tm) REVERT: S 3 GLN cc_start: 0.7592 (tt0) cc_final: 0.7149 (pt0) REVERT: S 39 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7216 (tp40) REVERT: S 179 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7244 (tm-30) REVERT: S 227 TYR cc_start: 0.7539 (m-10) cc_final: 0.6593 (m-10) REVERT: S 233 LEU cc_start: 0.8211 (tp) cc_final: 0.7873 (mt) outliers start: 28 outliers final: 9 residues processed: 178 average time/residue: 1.1991 time to fit residues: 227.7345 Evaluate side-chains 159 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain S residue 39 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 357 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9043 Z= 0.290 Angle : 0.580 7.753 12250 Z= 0.300 Chirality : 0.043 0.204 1400 Planarity : 0.004 0.030 1544 Dihedral : 5.308 56.539 1252 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.09 % Allowed : 24.03 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1119 helix: 1.27 (0.28), residues: 372 sheet: 0.06 (0.29), residues: 289 loop : -0.43 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 124 PHE 0.017 0.002 PHE B 253 TYR 0.021 0.002 TYR B 59 ARG 0.010 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.049 Fit side-chains REVERT: A 232 LEU cc_start: 0.8571 (mt) cc_final: 0.8020 (tp) REVERT: B 124 TYR cc_start: 0.8786 (m-80) cc_final: 0.8567 (m-80) REVERT: B 188 MET cc_start: 0.8624 (mmm) cc_final: 0.8303 (mmm) REVERT: B 189 SER cc_start: 0.8896 (t) cc_final: 0.8490 (t) REVERT: B 259 GLN cc_start: 0.7666 (pt0) cc_final: 0.7074 (pt0) REVERT: G 58 GLU cc_start: 0.8860 (mm-30) cc_final: 0.7998 (mp0) REVERT: G 62 ARG cc_start: 0.7280 (ttm110) cc_final: 0.7075 (mtm-85) REVERT: R 87 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5592 (ttt-90) REVERT: R 170 PHE cc_start: 0.8026 (p90) cc_final: 0.7090 (p90) REVERT: R 337 LEU cc_start: 0.8119 (mm) cc_final: 0.7915 (tm) REVERT: S 39 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7350 (tp40) REVERT: S 179 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: S 218 ARG cc_start: 0.6357 (ptp90) cc_final: 0.6136 (ptp90) REVERT: S 227 TYR cc_start: 0.7563 (m-10) cc_final: 0.6686 (m-10) outliers start: 39 outliers final: 19 residues processed: 172 average time/residue: 1.1639 time to fit residues: 213.8894 Evaluate side-chains 162 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 365 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 89 optimal weight: 0.0050 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 GLN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9043 Z= 0.167 Angle : 0.533 7.754 12250 Z= 0.274 Chirality : 0.041 0.166 1400 Planarity : 0.003 0.033 1544 Dihedral : 4.762 59.230 1248 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.46 % Allowed : 24.87 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1119 helix: 1.24 (0.28), residues: 375 sheet: 0.06 (0.29), residues: 292 loop : -0.39 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS R 83 PHE 0.015 0.001 PHE B 253 TYR 0.021 0.001 TYR B 59 ARG 0.009 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.106 Fit side-chains REVERT: A 232 LEU cc_start: 0.8576 (mt) cc_final: 0.8093 (tp) REVERT: B 129 ARG cc_start: 0.8475 (ptp-110) cc_final: 0.8211 (ptm-80) REVERT: B 188 MET cc_start: 0.8504 (mmm) cc_final: 0.8225 (mmm) REVERT: B 189 SER cc_start: 0.8811 (t) cc_final: 0.8435 (t) REVERT: B 217 MET cc_start: 0.8156 (tpp) cc_final: 0.7889 (ppp) REVERT: B 259 GLN cc_start: 0.7681 (pt0) cc_final: 0.7153 (pt0) REVERT: R 52 ARG cc_start: 0.8637 (mtp180) cc_final: 0.8328 (mtp180) REVERT: R 74 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8183 (tp-100) REVERT: R 81 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8610 (OUTLIER) REVERT: R 170 PHE cc_start: 0.7945 (p90) cc_final: 0.7068 (p90) REVERT: R 185 ILE cc_start: 0.8350 (mt) cc_final: 0.8097 (mt) REVERT: R 337 LEU cc_start: 0.8093 (mm) cc_final: 0.7873 (tm) REVERT: R 362 ASN cc_start: 0.8139 (t0) cc_final: 0.7724 (t0) REVERT: S 39 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7306 (tp40) REVERT: S 179 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7354 (tm-30) REVERT: S 227 TYR cc_start: 0.7586 (m-10) cc_final: 0.6758 (m-10) outliers start: 33 outliers final: 15 residues processed: 179 average time/residue: 1.1028 time to fit residues: 211.5864 Evaluate side-chains 161 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 230 ASN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9043 Z= 0.187 Angle : 0.548 7.934 12250 Z= 0.279 Chirality : 0.041 0.169 1400 Planarity : 0.003 0.038 1544 Dihedral : 4.684 55.655 1248 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.15 % Allowed : 26.55 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1119 helix: 1.28 (0.28), residues: 375 sheet: 0.12 (0.30), residues: 291 loop : -0.43 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 83 PHE 0.015 0.001 PHE B 253 TYR 0.023 0.001 TYR B 59 ARG 0.010 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8571 (mt) cc_final: 0.8080 (tp) REVERT: A 330 LYS cc_start: 0.8738 (mmtp) cc_final: 0.8327 (mppt) REVERT: B 188 MET cc_start: 0.8496 (mmm) cc_final: 0.8179 (mmm) REVERT: B 189 SER cc_start: 0.8886 (t) cc_final: 0.8514 (t) REVERT: B 212 ASP cc_start: 0.7796 (t0) cc_final: 0.7434 (t0) REVERT: B 259 GLN cc_start: 0.7720 (pt0) cc_final: 0.7162 (pt0) REVERT: G 58 GLU cc_start: 0.8820 (mm-30) cc_final: 0.7949 (mp0) REVERT: R 52 ARG cc_start: 0.8635 (mtp180) cc_final: 0.8318 (mtp180) REVERT: R 74 GLN cc_start: 0.8855 (tp-100) cc_final: 0.8098 (tp-100) REVERT: R 170 PHE cc_start: 0.7982 (p90) cc_final: 0.7088 (p90) REVERT: R 210 GLN cc_start: 0.7859 (mt0) cc_final: 0.7302 (mp10) REVERT: R 337 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7868 (tm) REVERT: R 362 ASN cc_start: 0.8258 (t0) cc_final: 0.7838 (t0) REVERT: S 39 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7317 (tp40) REVERT: S 59 TYR cc_start: 0.7027 (m-10) cc_final: 0.6784 (m-80) REVERT: S 179 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: S 223 ASP cc_start: 0.5806 (m-30) cc_final: 0.5530 (m-30) REVERT: S 227 TYR cc_start: 0.7575 (m-10) cc_final: 0.6725 (m-10) REVERT: S 233 LEU cc_start: 0.8225 (tp) cc_final: 0.7969 (mt) outliers start: 30 outliers final: 21 residues processed: 175 average time/residue: 1.1830 time to fit residues: 220.9282 Evaluate side-chains 165 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 230 ASN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9043 Z= 0.171 Angle : 0.552 8.042 12250 Z= 0.280 Chirality : 0.041 0.162 1400 Planarity : 0.003 0.040 1544 Dihedral : 4.625 53.197 1248 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.04 % Allowed : 26.65 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1119 helix: 1.31 (0.28), residues: 375 sheet: 0.13 (0.30), residues: 287 loop : -0.41 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS R 83 PHE 0.015 0.001 PHE B 253 TYR 0.026 0.001 TYR B 59 ARG 0.010 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.234 Fit side-chains REVERT: A 232 LEU cc_start: 0.8540 (mt) cc_final: 0.8077 (tp) REVERT: A 318 GLU cc_start: 0.8014 (tt0) cc_final: 0.7549 (pm20) REVERT: A 330 LYS cc_start: 0.8741 (mmtp) cc_final: 0.8354 (mppt) REVERT: B 188 MET cc_start: 0.8478 (mmm) cc_final: 0.8187 (mmm) REVERT: B 189 SER cc_start: 0.8887 (t) cc_final: 0.8521 (t) REVERT: B 212 ASP cc_start: 0.7890 (t0) cc_final: 0.7368 (t0) REVERT: B 259 GLN cc_start: 0.7658 (pt0) cc_final: 0.7111 (pt0) REVERT: B 292 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: G 38 MET cc_start: 0.8095 (ttm) cc_final: 0.7129 (ttm) REVERT: G 42 GLU cc_start: 0.7899 (pp20) cc_final: 0.7409 (pm20) REVERT: G 58 GLU cc_start: 0.8814 (mm-30) cc_final: 0.7954 (mp0) REVERT: R 52 ARG cc_start: 0.8645 (mtp180) cc_final: 0.8323 (mtp180) REVERT: R 74 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8265 (tp-100) REVERT: R 81 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: R 170 PHE cc_start: 0.7981 (p90) cc_final: 0.7124 (p90) REVERT: R 337 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7862 (tm) REVERT: R 362 ASN cc_start: 0.8197 (t0) cc_final: 0.7747 (t0) REVERT: S 39 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7309 (tp40) REVERT: S 179 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7400 (tm-30) REVERT: S 223 ASP cc_start: 0.5693 (m-30) cc_final: 0.5487 (m-30) REVERT: S 227 TYR cc_start: 0.7566 (m-10) cc_final: 0.6729 (m-10) REVERT: S 233 LEU cc_start: 0.8238 (tp) cc_final: 0.7996 (mt) outliers start: 29 outliers final: 15 residues processed: 175 average time/residue: 1.0832 time to fit residues: 203.9444 Evaluate side-chains 165 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 230 ASN R 74 GLN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9043 Z= 0.187 Angle : 0.554 8.639 12250 Z= 0.282 Chirality : 0.042 0.160 1400 Planarity : 0.003 0.035 1544 Dihedral : 4.583 50.912 1248 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.83 % Allowed : 27.49 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1119 helix: 1.44 (0.28), residues: 369 sheet: 0.07 (0.29), residues: 291 loop : -0.36 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 83 PHE 0.014 0.001 PHE B 253 TYR 0.028 0.001 TYR B 59 ARG 0.008 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8468 (mt) cc_final: 0.8012 (tp) REVERT: A 330 LYS cc_start: 0.8735 (mmtp) cc_final: 0.8326 (mppt) REVERT: B 44 GLN cc_start: 0.8790 (tt0) cc_final: 0.8532 (tp40) REVERT: B 188 MET cc_start: 0.8487 (mmm) cc_final: 0.8191 (mmm) REVERT: B 189 SER cc_start: 0.8900 (t) cc_final: 0.8529 (t) REVERT: B 212 ASP cc_start: 0.7891 (t0) cc_final: 0.7337 (t0) REVERT: B 259 GLN cc_start: 0.7722 (pt0) cc_final: 0.7176 (pt0) REVERT: B 292 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: G 38 MET cc_start: 0.8067 (ttm) cc_final: 0.7024 (ttm) REVERT: G 42 GLU cc_start: 0.7875 (pp20) cc_final: 0.7396 (pm20) REVERT: G 58 GLU cc_start: 0.8818 (mm-30) cc_final: 0.7973 (mp0) REVERT: R 74 GLN cc_start: 0.8884 (tp40) cc_final: 0.8265 (tp-100) REVERT: R 170 PHE cc_start: 0.7961 (p90) cc_final: 0.7083 (p90) REVERT: R 210 GLN cc_start: 0.7820 (mt0) cc_final: 0.7211 (mp10) REVERT: R 337 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7858 (tm) REVERT: R 362 ASN cc_start: 0.8238 (t0) cc_final: 0.7800 (t0) REVERT: S 39 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7326 (tp40) REVERT: S 179 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: S 223 ASP cc_start: 0.5656 (m-30) cc_final: 0.5439 (m-30) REVERT: S 227 TYR cc_start: 0.7567 (m-10) cc_final: 0.6728 (m-10) outliers start: 27 outliers final: 19 residues processed: 170 average time/residue: 1.1589 time to fit residues: 210.4458 Evaluate side-chains 167 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 230 ASN R 74 GLN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9043 Z= 0.219 Angle : 0.574 8.434 12250 Z= 0.291 Chirality : 0.042 0.166 1400 Planarity : 0.003 0.037 1544 Dihedral : 4.661 48.683 1248 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.73 % Allowed : 27.49 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1119 helix: 1.34 (0.28), residues: 368 sheet: 0.03 (0.30), residues: 292 loop : -0.38 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS R 83 PHE 0.015 0.001 PHE B 253 TYR 0.033 0.001 TYR B 59 ARG 0.008 0.001 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8440 (mt) cc_final: 0.7981 (tp) REVERT: A 330 LYS cc_start: 0.8730 (mmtp) cc_final: 0.8334 (mppt) REVERT: B 44 GLN cc_start: 0.8785 (tt0) cc_final: 0.8529 (tp40) REVERT: B 188 MET cc_start: 0.8515 (mmm) cc_final: 0.8250 (mmm) REVERT: B 189 SER cc_start: 0.8913 (t) cc_final: 0.8526 (t) REVERT: B 212 ASP cc_start: 0.7926 (t0) cc_final: 0.7364 (t0) REVERT: B 259 GLN cc_start: 0.7739 (pt0) cc_final: 0.7200 (pt0) REVERT: B 292 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: G 58 GLU cc_start: 0.8821 (mm-30) cc_final: 0.7976 (mp0) REVERT: R 52 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8065 (mpp80) REVERT: R 74 GLN cc_start: 0.8863 (tp-100) cc_final: 0.8393 (tp-100) REVERT: R 170 PHE cc_start: 0.8000 (p90) cc_final: 0.7108 (p90) REVERT: R 210 GLN cc_start: 0.7801 (mt0) cc_final: 0.7250 (mp10) REVERT: R 337 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7882 (tm) REVERT: S 39 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7353 (tp40) REVERT: S 179 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: S 223 ASP cc_start: 0.5613 (m-30) cc_final: 0.5398 (m-30) REVERT: S 227 TYR cc_start: 0.7575 (m-10) cc_final: 0.6750 (m-10) outliers start: 26 outliers final: 19 residues processed: 170 average time/residue: 1.1964 time to fit residues: 217.2880 Evaluate side-chains 171 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 230 ASN R 74 GLN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.166268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118931 restraints weight = 11919.404| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.89 r_work: 0.3333 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9043 Z= 0.169 Angle : 0.566 11.667 12250 Z= 0.286 Chirality : 0.041 0.155 1400 Planarity : 0.003 0.036 1544 Dihedral : 4.543 46.951 1248 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.62 % Allowed : 27.39 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1119 helix: 1.38 (0.28), residues: 368 sheet: 0.08 (0.29), residues: 290 loop : -0.34 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS R 83 PHE 0.014 0.001 PHE B 253 TYR 0.019 0.001 TYR B 59 ARG 0.008 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4154.90 seconds wall clock time: 74 minutes 12.76 seconds (4452.76 seconds total)