Starting phenix.real_space_refine on Mon Mar 11 17:04:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/03_2024/6so5_10266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/03_2024/6so5_10266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/03_2024/6so5_10266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/03_2024/6so5_10266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/03_2024/6so5_10266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/03_2024/6so5_10266.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 73 5.16 5 C 5673 2.51 5 N 1425 2.21 5 O 1565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8737 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2464 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain breaks: 1 Chain: "B" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2301 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 17, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1160 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain breaks: 1 Chain: "D" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1160 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain breaks: 1 Chain: "E" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 835 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 816 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4310 SG CYS B 289 46.170 112.721 80.191 1.00101.14 S ATOM 4333 SG CYS B 292 44.838 111.737 77.378 1.00 91.48 S Time building chain proxies: 4.93, per 1000 atoms: 0.56 Number of scatterers: 8737 At special positions: 0 Unit cell: (87.48, 129.6, 106.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 73 16.00 O 1565 8.00 N 1425 7.00 C 5673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 284 " distance=1.75 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: 3.71 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 289 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 292 " 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 3 sheets defined 71.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 removed outlier: 4.006A pdb=" N ILE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.970A pdb=" N ASP A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 removed outlier: 4.177A pdb=" N LEU A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 125 through 139 removed outlier: 3.517A pdb=" N LYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 159 removed outlier: 4.043A pdb=" N VAL A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 203 removed outlier: 3.838A pdb=" N THR A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 215 through 238 removed outlier: 4.053A pdb=" N ALA A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.543A pdb=" N ASP A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 289 through 310 removed outlier: 3.558A pdb=" N ASP A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 4.087A pdb=" N LYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 49 through 64 Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.586A pdb=" N ASP B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.765A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 128 through 134 removed outlier: 4.476A pdb=" N GLU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 157 Processing helix chain 'B' and resid 175 through 182 Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.597A pdb=" N LEU B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.661A pdb=" N THR B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 289 through 308 removed outlier: 3.610A pdb=" N ASP B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 removed outlier: 4.217A pdb=" N VAL B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 27 removed outlier: 3.740A pdb=" N ASN C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 61 removed outlier: 3.519A pdb=" N PHE C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS C 41 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 124 Processing helix chain 'C' and resid 150 through 171 removed outlier: 4.457A pdb=" N CYS C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS C 162 " --> pdb=" O TRP C 158 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 28 removed outlier: 3.999A pdb=" N TRP D 11 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU D 15 " --> pdb=" O TRP D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 62 Processing helix chain 'D' and resid 64 through 124 removed outlier: 8.319A pdb=" N ALA D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ARG D 71 " --> pdb=" O ASP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 171 Processing helix chain 'E' and resid 190 through 208 removed outlier: 5.063A pdb=" N ALA E 205 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE E 206 " --> pdb=" O GLY E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 231 removed outlier: 3.951A pdb=" N THR E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR E 228 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 251 Processing helix chain 'E' and resid 253 through 291 removed outlier: 4.029A pdb=" N MET E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 209 removed outlier: 3.562A pdb=" N LEU F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 229 removed outlier: 3.568A pdb=" N THR F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 251 Processing helix chain 'F' and resid 252 through 291 removed outlier: 3.575A pdb=" N VAL F 256 " --> pdb=" O ILE F 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F 257 " --> pdb=" O PRO F 253 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 removed outlier: 6.859A pdb=" N LEU A 69 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 242 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N ASN A 274 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 244 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE A 276 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS A 246 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 70 removed outlier: 6.227A pdb=" N LEU B 69 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 43 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR B 272 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE B 244 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN B 274 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 246 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N HIS B 273 " --> pdb=" O HIS B 314 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL B 316 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1689 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: 2.24 Time building geometry restraints manager: 3.98 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: 2719 1.34 - 1.46: 2033 1.46 - 1.58: 4049 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 8918 Sorted by residual: bond pdb=" N CYS F 208 " pdb=" CA CYS F 208 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.31e-02 5.83e+03 7.41e+00 bond pdb=" N LYS F 209 " pdb=" CA LYS F 209 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.70e+00 bond pdb=" N TYR F 210 " pdb=" CA TYR F 210 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.28e-02 6.10e+03 5.44e+00 bond pdb=" CA LEU B 28 " pdb=" C LEU B 28 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.72e-02 3.38e+03 3.15e+00 bond pdb=" C ASP B 74 " pdb=" N PRO B 75 " ideal model delta sigma weight residual 1.337 1.322 0.014 9.80e-03 1.04e+04 2.11e+00 ... (remaining 8913 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.69: 201 105.69 - 112.78: 4844 112.78 - 119.87: 2938 119.87 - 126.96: 3963 126.96 - 134.05: 99 Bond angle restraints: 12045 Sorted by residual: angle pdb=" C LEU E 274 " pdb=" N CYS E 275 " pdb=" CA CYS E 275 " ideal model delta sigma weight residual 122.38 112.49 9.89 1.81e+00 3.05e-01 2.99e+01 angle pdb=" N ILE E 190 " pdb=" CA ILE E 190 " pdb=" C ILE E 190 " ideal model delta sigma weight residual 111.91 107.69 4.22 8.90e-01 1.26e+00 2.25e+01 angle pdb=" CA CYS E 275 " pdb=" CB CYS E 275 " pdb=" SG CYS E 275 " ideal model delta sigma weight residual 114.40 123.08 -8.68 2.30e+00 1.89e-01 1.42e+01 angle pdb=" N CYS F 208 " pdb=" CA CYS F 208 " pdb=" C CYS F 208 " ideal model delta sigma weight residual 113.18 108.71 4.47 1.21e+00 6.83e-01 1.36e+01 angle pdb=" N ALA C 6 " pdb=" CA ALA C 6 " pdb=" C ALA C 6 " ideal model delta sigma weight residual 111.82 107.62 4.20 1.16e+00 7.43e-01 1.31e+01 ... (remaining 12040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 4663 16.21 - 32.42: 596 32.42 - 48.62: 124 48.62 - 64.83: 21 64.83 - 81.04: 8 Dihedral angle restraints: 5412 sinusoidal: 2193 harmonic: 3219 Sorted by residual: dihedral pdb=" CB CYS F 208 " pdb=" SG CYS F 208 " pdb=" SG CYS F 284 " pdb=" CB CYS F 284 " ideal model delta sinusoidal sigma weight residual -86.00 -155.23 69.23 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CA SER F 212 " pdb=" C SER F 212 " pdb=" N ILE F 213 " pdb=" CA ILE F 213 " ideal model delta harmonic sigma weight residual 180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA HIS E 285 " pdb=" C HIS E 285 " pdb=" N GLU E 286 " pdb=" CA GLU E 286 " ideal model delta harmonic sigma weight residual 180.00 157.32 22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 933 0.039 - 0.078: 330 0.078 - 0.117: 104 0.117 - 0.156: 15 0.156 - 0.195: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA CYS E 275 " pdb=" N CYS E 275 " pdb=" C CYS E 275 " pdb=" CB CYS E 275 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA PRO D 29 " pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CB PRO D 29 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CB ILE F 252 " pdb=" CA ILE F 252 " pdb=" CG1 ILE F 252 " pdb=" CG2 ILE F 252 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 1383 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 168 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.17e+00 pdb=" N PRO B 169 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 207 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.31e+00 pdb=" C VAL F 207 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL F 207 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS F 208 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 159 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C ILE D 159 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE D 159 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU D 160 " -0.012 2.00e-02 2.50e+03 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 130 2.56 - 3.14: 8344 3.14 - 3.73: 14458 3.73 - 4.31: 18665 4.31 - 4.90: 28255 Nonbonded interactions: 69852 Sorted by model distance: nonbonded pdb=" CG2 THR E 219 " pdb=" CE2 TYR E 277 " model vdw 1.973 3.760 nonbonded pdb=" OE1 GLU A 259 " pdb=" OH TYR A 310 " model vdw 2.149 2.440 nonbonded pdb=" OH TYR A 256 " pdb=" NH2 ARG A 260 " model vdw 2.196 2.520 nonbonded pdb=" OE2 GLU A 251 " pdb=" N SER A 254 " model vdw 2.220 2.520 nonbonded pdb=" OE2 GLU C 46 " pdb=" NE ARG C 50 " model vdw 2.223 2.520 ... (remaining 69847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 190 or resid 220 through 344)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 191 through 291) selection = chain 'F' } 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: 1.050 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: 5.470 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.010 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8918 Z= 0.340 Angle : 0.816 9.894 12045 Z= 0.466 Chirality : 0.044 0.195 1386 Planarity : 0.005 0.071 1497 Dihedral : 14.990 81.038 3308 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % 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: -4.60 (0.21), residues: 1077 helix: -2.53 (0.15), residues: 684 sheet: -4.50 (0.37), residues: 97 loop : -3.21 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 9 HIS 0.012 0.002 HIS A 296 PHE 0.016 0.002 PHE F 283 TYR 0.014 0.002 TYR E 224 ARG 0.005 0.000 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9192 (mm) cc_final: 0.8870 (tp) REVERT: A 124 MET cc_start: 0.2545 (ttp) cc_final: 0.2177 (tpp) REVERT: A 185 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8448 (tpm170) REVERT: A 189 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7755 (mmm160) REVERT: A 221 LYS cc_start: 0.9224 (mttt) cc_final: 0.8955 (mmmt) REVERT: A 241 GLN cc_start: 0.8011 (pt0) cc_final: 0.7765 (pt0) REVERT: A 257 GLU cc_start: 0.8290 (tp30) cc_final: 0.8023 (tm-30) REVERT: B 153 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8712 (mmm-85) REVERT: B 249 ILE cc_start: 0.9427 (mt) cc_final: 0.9149 (tt) REVERT: B 288 PRO cc_start: 0.7272 (Cg_endo) cc_final: 0.7041 (Cg_exo) REVERT: C 76 GLU cc_start: 0.8268 (tp30) cc_final: 0.8045 (tp30) REVERT: C 81 LYS cc_start: 0.9294 (tttt) cc_final: 0.9070 (ttmm) REVERT: C 155 ILE cc_start: 0.7736 (mt) cc_final: 0.7486 (mt) REVERT: D 13 LEU cc_start: 0.9003 (tp) cc_final: 0.8549 (tp) REVERT: D 17 PHE cc_start: 0.8789 (m-80) cc_final: 0.8561 (m-80) REVERT: D 19 PHE cc_start: 0.8746 (m-80) cc_final: 0.8175 (m-80) REVERT: D 31 PHE cc_start: 0.6747 (m-80) cc_final: 0.6474 (m-80) REVERT: D 49 MET cc_start: 0.8686 (mmm) cc_final: 0.8388 (mmm) REVERT: D 52 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8651 (mt-10) REVERT: D 53 ILE cc_start: 0.9635 (mt) cc_final: 0.9356 (mt) REVERT: D 56 MET cc_start: 0.8797 (ptp) cc_final: 0.8494 (mtm) REVERT: D 57 LYS cc_start: 0.9647 (mttt) cc_final: 0.9290 (mttp) REVERT: D 101 LYS cc_start: 0.9307 (tmtt) cc_final: 0.9029 (tmtt) REVERT: D 108 PHE cc_start: 0.8381 (t80) cc_final: 0.8142 (t80) REVERT: D 123 TYR cc_start: 0.7861 (p90) cc_final: 0.7619 (t80) REVERT: D 155 ILE cc_start: 0.9369 (mt) cc_final: 0.8812 (mt) REVERT: E 266 LYS cc_start: 0.8690 (mttt) cc_final: 0.8202 (mtmt) REVERT: E 273 ASP cc_start: 0.9214 (m-30) cc_final: 0.8807 (m-30) REVERT: E 274 LEU cc_start: 0.9001 (mm) cc_final: 0.8667 (mm) REVERT: F 225 MET cc_start: 0.8809 (mmt) cc_final: 0.8543 (mmt) REVERT: F 227 LEU cc_start: 0.9264 (mt) cc_final: 0.8924 (mm) REVERT: F 248 LEU cc_start: 0.7080 (pp) cc_final: 0.6838 (pp) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2469 time to fit residues: 106.9739 Evaluate side-chains 261 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 235 GLN B 332 ASN C 45 GLN C 89 HIS E 258 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8918 Z= 0.237 Angle : 0.688 9.180 12045 Z= 0.357 Chirality : 0.044 0.262 1386 Planarity : 0.005 0.060 1497 Dihedral : 5.222 22.279 1162 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.10 % Allowed : 5.88 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.24), residues: 1077 helix: -0.86 (0.18), residues: 681 sheet: -3.58 (0.45), residues: 91 loop : -2.68 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 158 HIS 0.004 0.001 HIS A 296 PHE 0.019 0.002 PHE F 278 TYR 0.031 0.002 TYR E 277 ARG 0.006 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 332 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9103 (mm) cc_final: 0.8869 (tp) REVERT: A 131 MET cc_start: 0.6911 (mmt) cc_final: 0.6617 (mmm) REVERT: A 158 MET cc_start: 0.7612 (tpt) cc_final: 0.7317 (tpt) REVERT: A 189 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7522 (mmm160) REVERT: A 221 LYS cc_start: 0.9229 (mttt) cc_final: 0.8997 (mmmt) REVERT: A 257 GLU cc_start: 0.8251 (tp30) cc_final: 0.7936 (tm-30) REVERT: B 101 PHE cc_start: 0.7720 (m-10) cc_final: 0.6609 (m-10) REVERT: B 152 MET cc_start: 0.8733 (mmm) cc_final: 0.8463 (mmm) REVERT: B 153 ARG cc_start: 0.8894 (mtt180) cc_final: 0.8530 (mmm-85) REVERT: C 59 GLU cc_start: 0.8754 (tp30) cc_final: 0.8516 (tp30) REVERT: C 157 CYS cc_start: 0.9307 (m) cc_final: 0.9075 (p) REVERT: D 13 LEU cc_start: 0.8913 (tp) cc_final: 0.8451 (tp) REVERT: D 17 PHE cc_start: 0.8762 (m-10) cc_final: 0.8561 (m-80) REVERT: D 19 PHE cc_start: 0.8615 (m-80) cc_final: 0.8392 (m-80) REVERT: D 49 MET cc_start: 0.8620 (mmm) cc_final: 0.8258 (mmm) REVERT: D 55 ASP cc_start: 0.8267 (t70) cc_final: 0.8018 (t70) REVERT: D 101 LYS cc_start: 0.9280 (tmtt) cc_final: 0.8997 (tmtt) REVERT: D 163 ASN cc_start: 0.8760 (m110) cc_final: 0.8358 (m110) REVERT: E 266 LYS cc_start: 0.8520 (mttt) cc_final: 0.8211 (mtmt) REVERT: E 273 ASP cc_start: 0.9142 (m-30) cc_final: 0.8865 (m-30) REVERT: F 225 MET cc_start: 0.8845 (mmt) cc_final: 0.8630 (mmm) REVERT: F 227 LEU cc_start: 0.8598 (mt) cc_final: 0.8307 (tp) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.2189 time to fit residues: 97.1162 Evaluate side-chains 269 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.0570 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8918 Z= 0.196 Angle : 0.666 9.226 12045 Z= 0.344 Chirality : 0.044 0.256 1386 Planarity : 0.005 0.055 1497 Dihedral : 4.946 18.660 1162 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.21 % Allowed : 4.44 % Favored : 95.36 % 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 (0.25), residues: 1077 helix: 0.03 (0.19), residues: 709 sheet: -3.05 (0.47), residues: 92 loop : -2.45 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 158 HIS 0.004 0.001 HIS B 314 PHE 0.027 0.002 PHE F 271 TYR 0.019 0.002 TYR E 277 ARG 0.003 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 342 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.8385 (m) cc_final: 0.8167 (p) REVERT: B 60 GLN cc_start: 0.7837 (mm110) cc_final: 0.7504 (mm110) REVERT: B 101 PHE cc_start: 0.7666 (m-10) cc_final: 0.7386 (m-10) REVERT: B 152 MET cc_start: 0.8657 (mmm) cc_final: 0.8394 (mmm) REVERT: B 235 GLN cc_start: 0.9108 (mt0) cc_final: 0.8731 (mt0) REVERT: C 48 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8423 (tm-30) REVERT: C 49 MET cc_start: 0.8604 (mpp) cc_final: 0.8322 (mmm) REVERT: C 60 LEU cc_start: 0.9065 (tt) cc_final: 0.8622 (tt) REVERT: C 72 TYR cc_start: 0.8097 (t80) cc_final: 0.7869 (t80) REVERT: C 157 CYS cc_start: 0.9290 (m) cc_final: 0.9077 (p) REVERT: D 13 LEU cc_start: 0.8890 (tp) cc_final: 0.8234 (tp) REVERT: D 49 MET cc_start: 0.8716 (mmm) cc_final: 0.8209 (mmm) REVERT: D 55 ASP cc_start: 0.8385 (t70) cc_final: 0.8148 (t70) REVERT: D 68 GLU cc_start: 0.7299 (tp30) cc_final: 0.6587 (tp30) REVERT: D 72 TYR cc_start: 0.7991 (t80) cc_final: 0.7682 (t80) REVERT: D 124 TYR cc_start: 0.6059 (m-10) cc_final: 0.5451 (m-80) REVERT: D 155 ILE cc_start: 0.9390 (mt) cc_final: 0.8881 (mt) REVERT: D 163 ASN cc_start: 0.8712 (m110) cc_final: 0.8179 (m110) REVERT: E 273 ASP cc_start: 0.9270 (m-30) cc_final: 0.8841 (m-30) REVERT: E 274 LEU cc_start: 0.8983 (mm) cc_final: 0.8755 (mm) REVERT: F 221 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8635 (tp-100) REVERT: F 225 MET cc_start: 0.9029 (mmt) cc_final: 0.8341 (mmm) REVERT: F 227 LEU cc_start: 0.8772 (mt) cc_final: 0.8379 (tp) outliers start: 2 outliers final: 1 residues processed: 343 average time/residue: 0.2101 time to fit residues: 97.1192 Evaluate side-chains 272 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 104 optimal weight: 0.0020 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8918 Z= 0.200 Angle : 0.665 9.435 12045 Z= 0.339 Chirality : 0.044 0.303 1386 Planarity : 0.005 0.058 1497 Dihedral : 4.761 20.484 1162 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 1077 helix: 0.43 (0.19), residues: 699 sheet: -2.76 (0.49), residues: 92 loop : -2.20 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP D 158 HIS 0.003 0.001 HIS E 285 PHE 0.028 0.002 PHE D 19 TYR 0.017 0.001 TYR E 277 ARG 0.007 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7232 (mtt180) REVERT: A 221 LYS cc_start: 0.9355 (mmtm) cc_final: 0.9061 (mmmt) REVERT: A 295 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7869 (ttm-80) REVERT: B 60 GLN cc_start: 0.7839 (mm110) cc_final: 0.7519 (mm110) REVERT: B 101 PHE cc_start: 0.7783 (m-10) cc_final: 0.7417 (m-10) REVERT: B 152 MET cc_start: 0.8708 (mmm) cc_final: 0.8406 (mmm) REVERT: C 58 GLN cc_start: 0.8500 (pp30) cc_final: 0.7783 (tm-30) REVERT: C 60 LEU cc_start: 0.9000 (tt) cc_final: 0.8029 (tt) REVERT: C 82 MET cc_start: 0.8617 (mpp) cc_final: 0.8359 (mpp) REVERT: C 86 LEU cc_start: 0.9370 (pp) cc_final: 0.8668 (pp) REVERT: C 159 ILE cc_start: 0.9361 (pt) cc_final: 0.9096 (pt) REVERT: D 19 PHE cc_start: 0.8501 (m-80) cc_final: 0.8103 (m-80) REVERT: D 49 MET cc_start: 0.8656 (mmm) cc_final: 0.8336 (mmm) REVERT: D 55 ASP cc_start: 0.8326 (t70) cc_final: 0.7965 (t70) REVERT: D 59 GLU cc_start: 0.8874 (pt0) cc_final: 0.8286 (pt0) REVERT: D 72 TYR cc_start: 0.7990 (t80) cc_final: 0.7771 (t80) REVERT: D 91 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8803 (ptpp) REVERT: D 155 ILE cc_start: 0.9358 (mt) cc_final: 0.9064 (mt) REVERT: D 163 ASN cc_start: 0.8694 (m110) cc_final: 0.8007 (m110) REVERT: E 189 ARG cc_start: 0.7038 (ptt180) cc_final: 0.6691 (ptt-90) REVERT: E 273 ASP cc_start: 0.9313 (m-30) cc_final: 0.8755 (m-30) REVERT: E 277 TYR cc_start: 0.8159 (m-80) cc_final: 0.7906 (m-80) REVERT: F 221 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8567 (tp-100) REVERT: F 225 MET cc_start: 0.9055 (mmt) cc_final: 0.8131 (mmm) REVERT: F 227 LEU cc_start: 0.8782 (mt) cc_final: 0.8338 (tp) REVERT: F 229 LYS cc_start: 0.8556 (mppt) cc_final: 0.8316 (tptt) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2127 time to fit residues: 95.1788 Evaluate side-chains 268 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8918 Z= 0.395 Angle : 0.805 9.578 12045 Z= 0.421 Chirality : 0.048 0.289 1386 Planarity : 0.006 0.065 1497 Dihedral : 5.249 23.188 1162 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % 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: -1.29 (0.26), residues: 1077 helix: 0.02 (0.19), residues: 709 sheet: -3.29 (0.46), residues: 95 loop : -1.94 (0.42), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP D 158 HIS 0.009 0.002 HIS A 77 PHE 0.032 0.002 PHE D 19 TYR 0.027 0.002 TYR A 148 ARG 0.007 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8884 (tmm) cc_final: 0.7875 (tmm) REVERT: A 105 ILE cc_start: 0.9192 (mm) cc_final: 0.8934 (tp) REVERT: A 295 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: B 60 GLN cc_start: 0.7981 (mm110) cc_final: 0.7663 (mm110) REVERT: B 69 LEU cc_start: 0.9034 (tp) cc_final: 0.8780 (tp) REVERT: B 101 PHE cc_start: 0.8001 (m-10) cc_final: 0.7751 (m-10) REVERT: B 152 MET cc_start: 0.8814 (mmm) cc_final: 0.8511 (mmm) REVERT: B 315 ILE cc_start: 0.8642 (mp) cc_final: 0.8439 (mp) REVERT: C 66 MET cc_start: 0.8068 (tpp) cc_final: 0.7382 (tpt) REVERT: C 86 LEU cc_start: 0.9601 (pp) cc_final: 0.9373 (pp) REVERT: D 49 MET cc_start: 0.8795 (mmm) cc_final: 0.8407 (mmm) REVERT: D 55 ASP cc_start: 0.8367 (t70) cc_final: 0.7992 (t70) REVERT: D 59 GLU cc_start: 0.8877 (pt0) cc_final: 0.8361 (pt0) REVERT: D 72 TYR cc_start: 0.7962 (t80) cc_final: 0.7742 (t80) REVERT: D 91 LYS cc_start: 0.9221 (mtpp) cc_final: 0.9020 (mmmt) REVERT: D 108 PHE cc_start: 0.8169 (t80) cc_final: 0.7964 (t80) REVERT: D 155 ILE cc_start: 0.9379 (mt) cc_final: 0.9166 (mt) REVERT: D 163 ASN cc_start: 0.8609 (m110) cc_final: 0.8257 (m110) REVERT: E 221 GLN cc_start: 0.8512 (mp10) cc_final: 0.7834 (mp10) REVERT: E 266 LYS cc_start: 0.8509 (mttt) cc_final: 0.8156 (mtmt) REVERT: E 273 ASP cc_start: 0.9338 (m-30) cc_final: 0.9086 (m-30) REVERT: E 277 TYR cc_start: 0.8326 (m-80) cc_final: 0.8117 (m-80) REVERT: F 221 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8406 (tp-100) REVERT: F 225 MET cc_start: 0.9046 (mmt) cc_final: 0.8098 (mmm) REVERT: F 229 LYS cc_start: 0.8528 (mppt) cc_final: 0.8174 (tptt) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.2093 time to fit residues: 81.7435 Evaluate side-chains 249 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8918 Z= 0.251 Angle : 0.717 10.075 12045 Z= 0.369 Chirality : 0.046 0.312 1386 Planarity : 0.005 0.064 1497 Dihedral : 5.040 22.388 1162 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.21 % 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: -0.99 (0.26), residues: 1077 helix: 0.29 (0.19), residues: 709 sheet: -3.09 (0.49), residues: 95 loop : -2.01 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP D 158 HIS 0.008 0.001 HIS A 296 PHE 0.035 0.002 PHE D 19 TYR 0.028 0.002 TYR F 277 ARG 0.010 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8846 (tmm) cc_final: 0.8156 (tmm) REVERT: A 105 ILE cc_start: 0.9086 (mm) cc_final: 0.8879 (tp) REVERT: B 50 LYS cc_start: 0.8566 (pttt) cc_final: 0.8273 (ptmt) REVERT: B 101 PHE cc_start: 0.8099 (m-10) cc_final: 0.7642 (m-10) REVERT: B 152 MET cc_start: 0.8737 (mmm) cc_final: 0.8436 (mmm) REVERT: B 241 GLN cc_start: 0.7418 (pt0) cc_final: 0.6995 (pt0) REVERT: B 293 GLU cc_start: 0.8157 (pp20) cc_final: 0.7781 (tm-30) REVERT: C 49 MET cc_start: 0.9360 (ttp) cc_final: 0.9130 (ttp) REVERT: C 52 GLU cc_start: 0.8479 (pt0) cc_final: 0.8143 (pt0) REVERT: C 60 LEU cc_start: 0.9174 (tt) cc_final: 0.8680 (tt) REVERT: D 17 PHE cc_start: 0.8769 (m-80) cc_final: 0.8416 (m-80) REVERT: D 19 PHE cc_start: 0.8565 (m-80) cc_final: 0.8286 (m-80) REVERT: D 49 MET cc_start: 0.8799 (mmm) cc_final: 0.8406 (mmm) REVERT: D 55 ASP cc_start: 0.8337 (t70) cc_final: 0.7995 (t70) REVERT: D 59 GLU cc_start: 0.8890 (pt0) cc_final: 0.8397 (pt0) REVERT: D 72 TYR cc_start: 0.8106 (t80) cc_final: 0.7864 (t80) REVERT: D 76 GLU cc_start: 0.8295 (mp0) cc_final: 0.8056 (mp0) REVERT: D 155 ILE cc_start: 0.9385 (mt) cc_final: 0.9139 (mt) REVERT: D 163 ASN cc_start: 0.8500 (m110) cc_final: 0.8075 (m110) REVERT: E 221 GLN cc_start: 0.8460 (mp10) cc_final: 0.7901 (mp10) REVERT: E 273 ASP cc_start: 0.9298 (m-30) cc_final: 0.8759 (m-30) REVERT: E 277 TYR cc_start: 0.8060 (m-80) cc_final: 0.7772 (m-80) REVERT: F 221 GLN cc_start: 0.8938 (tp-100) cc_final: 0.8329 (tp-100) REVERT: F 225 MET cc_start: 0.9050 (mmt) cc_final: 0.8249 (mmm) REVERT: F 229 LYS cc_start: 0.8571 (mppt) cc_final: 0.8351 (tptt) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.2067 time to fit residues: 85.4185 Evaluate side-chains 262 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 0.0670 chunk 104 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 235 GLN A 274 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN F 285 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8918 Z= 0.192 Angle : 0.706 10.064 12045 Z= 0.359 Chirality : 0.046 0.319 1386 Planarity : 0.005 0.069 1497 Dihedral : 4.839 20.600 1162 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.10 % Allowed : 1.75 % Favored : 98.14 % 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: -0.59 (0.26), residues: 1077 helix: 0.60 (0.19), residues: 712 sheet: -2.64 (0.52), residues: 95 loop : -2.02 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP D 158 HIS 0.005 0.001 HIS F 285 PHE 0.022 0.002 PHE D 19 TYR 0.019 0.001 TYR E 277 ARG 0.010 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TYR cc_start: 0.7980 (m-80) cc_final: 0.7740 (m-80) REVERT: A 103 MET cc_start: 0.8871 (tmm) cc_final: 0.8118 (tmm) REVERT: A 222 LEU cc_start: 0.9275 (mt) cc_final: 0.8916 (pp) REVERT: A 318 LEU cc_start: 0.9575 (tp) cc_final: 0.9334 (tt) REVERT: B 50 LYS cc_start: 0.8427 (pttt) cc_final: 0.8158 (ptmt) REVERT: B 152 MET cc_start: 0.8684 (mmm) cc_final: 0.8186 (mmm) REVERT: B 241 GLN cc_start: 0.7179 (pt0) cc_final: 0.6724 (pt0) REVERT: B 293 GLU cc_start: 0.8100 (pp20) cc_final: 0.7869 (tm-30) REVERT: B 295 ARG cc_start: 0.8248 (mmm160) cc_final: 0.7735 (mmm160) REVERT: C 49 MET cc_start: 0.9367 (ttp) cc_final: 0.9078 (ttp) REVERT: C 52 GLU cc_start: 0.8351 (pt0) cc_final: 0.7854 (pt0) REVERT: C 58 GLN cc_start: 0.8474 (pp30) cc_final: 0.7724 (tm-30) REVERT: C 60 LEU cc_start: 0.9118 (tt) cc_final: 0.8348 (tp) REVERT: D 49 MET cc_start: 0.8790 (mmm) cc_final: 0.8388 (mmm) REVERT: D 55 ASP cc_start: 0.8373 (t70) cc_final: 0.7947 (t70) REVERT: D 57 LYS cc_start: 0.9631 (mttt) cc_final: 0.9329 (mtmm) REVERT: D 59 GLU cc_start: 0.8871 (pt0) cc_final: 0.8360 (pt0) REVERT: D 72 TYR cc_start: 0.8110 (t80) cc_final: 0.7892 (t80) REVERT: D 101 LYS cc_start: 0.9247 (tmtt) cc_final: 0.8946 (tmtt) REVERT: D 155 ILE cc_start: 0.9355 (mt) cc_final: 0.9149 (mt) REVERT: D 163 ASN cc_start: 0.8373 (m110) cc_final: 0.8011 (m110) REVERT: E 273 ASP cc_start: 0.9258 (m-30) cc_final: 0.8630 (m-30) REVERT: E 274 LEU cc_start: 0.8962 (mm) cc_final: 0.8714 (mm) REVERT: F 221 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8236 (tp-100) REVERT: F 225 MET cc_start: 0.9001 (mmt) cc_final: 0.8193 (mmm) outliers start: 1 outliers final: 1 residues processed: 328 average time/residue: 0.2116 time to fit residues: 92.9685 Evaluate side-chains 268 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8918 Z= 0.196 Angle : 0.711 8.515 12045 Z= 0.362 Chirality : 0.046 0.314 1386 Planarity : 0.005 0.070 1497 Dihedral : 4.741 20.375 1162 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -0.60 (0.26), residues: 1077 helix: 0.61 (0.19), residues: 712 sheet: -2.28 (0.54), residues: 93 loop : -2.25 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.002 TRP D 158 HIS 0.005 0.001 HIS E 285 PHE 0.028 0.002 PHE D 19 TYR 0.028 0.001 TYR E 277 ARG 0.012 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8919 (tmm) cc_final: 0.7734 (tmm) REVERT: A 185 ARG cc_start: 0.8392 (tpt90) cc_final: 0.7886 (tpm170) REVERT: B 50 LYS cc_start: 0.8344 (pttt) cc_final: 0.8095 (ptmt) REVERT: B 92 THR cc_start: 0.8352 (p) cc_final: 0.8058 (p) REVERT: B 152 MET cc_start: 0.8622 (mmm) cc_final: 0.8299 (mmm) REVERT: B 185 ARG cc_start: 0.6730 (tmt170) cc_final: 0.6520 (tpm170) REVERT: B 241 GLN cc_start: 0.7222 (pt0) cc_final: 0.6765 (pt0) REVERT: B 293 GLU cc_start: 0.8085 (pp20) cc_final: 0.7849 (tm-30) REVERT: C 49 MET cc_start: 0.9369 (ttp) cc_final: 0.8775 (ttp) REVERT: C 53 ILE cc_start: 0.9351 (mm) cc_final: 0.8885 (mm) REVERT: C 58 GLN cc_start: 0.8489 (pp30) cc_final: 0.7809 (tm-30) REVERT: C 76 GLU cc_start: 0.8282 (mp0) cc_final: 0.8079 (mp0) REVERT: D 49 MET cc_start: 0.8582 (mmm) cc_final: 0.8379 (mmm) REVERT: D 55 ASP cc_start: 0.8267 (t70) cc_final: 0.7871 (t70) REVERT: D 59 GLU cc_start: 0.8815 (pt0) cc_final: 0.8264 (pt0) REVERT: D 72 TYR cc_start: 0.8097 (t80) cc_final: 0.7816 (t80) REVERT: D 91 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8838 (ptpp) REVERT: D 112 GLN cc_start: 0.8279 (tt0) cc_final: 0.8042 (tt0) REVERT: D 116 MET cc_start: 0.8919 (ptp) cc_final: 0.8661 (ptp) REVERT: D 163 ASN cc_start: 0.8247 (m110) cc_final: 0.7895 (m110) REVERT: E 204 ARG cc_start: 0.8201 (ppt170) cc_final: 0.7889 (ppt170) REVERT: E 221 GLN cc_start: 0.8278 (mp10) cc_final: 0.7742 (mp10) REVERT: E 273 ASP cc_start: 0.9327 (m-30) cc_final: 0.8823 (m-30) REVERT: E 274 LEU cc_start: 0.8953 (mm) cc_final: 0.8732 (mm) REVERT: E 277 TYR cc_start: 0.7987 (m-80) cc_final: 0.7729 (m-80) REVERT: F 221 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8091 (tp-100) REVERT: F 225 MET cc_start: 0.8947 (mmt) cc_final: 0.8150 (mmm) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2052 time to fit residues: 89.0569 Evaluate side-chains 258 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8918 Z= 0.224 Angle : 0.725 8.132 12045 Z= 0.372 Chirality : 0.045 0.313 1386 Planarity : 0.005 0.066 1497 Dihedral : 4.726 19.603 1162 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 1077 helix: 0.64 (0.19), residues: 699 sheet: -2.29 (0.53), residues: 91 loop : -1.60 (0.40), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP D 158 HIS 0.010 0.001 HIS E 285 PHE 0.029 0.002 PHE D 19 TYR 0.031 0.001 TYR E 277 ARG 0.013 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8837 (tmm) cc_final: 0.8106 (tmm) REVERT: A 185 ARG cc_start: 0.8416 (tpt90) cc_final: 0.7883 (tpm170) REVERT: A 318 LEU cc_start: 0.9442 (tt) cc_final: 0.9199 (tt) REVERT: B 50 LYS cc_start: 0.8407 (pttt) cc_final: 0.8143 (ptmt) REVERT: B 152 MET cc_start: 0.8563 (mmm) cc_final: 0.8227 (mmm) REVERT: B 185 ARG cc_start: 0.6738 (tmt170) cc_final: 0.6492 (tpm170) REVERT: B 241 GLN cc_start: 0.7286 (pt0) cc_final: 0.6856 (pt0) REVERT: B 293 GLU cc_start: 0.8098 (pp20) cc_final: 0.7852 (tm-30) REVERT: C 48 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8771 (tm-30) REVERT: C 49 MET cc_start: 0.9400 (ttp) cc_final: 0.9137 (ttp) REVERT: C 58 GLN cc_start: 0.8449 (pp30) cc_final: 0.7864 (tm-30) REVERT: C 61 SER cc_start: 0.9329 (m) cc_final: 0.9107 (t) REVERT: D 9 TRP cc_start: 0.5041 (m-10) cc_final: 0.4705 (m-10) REVERT: D 12 LEU cc_start: 0.8699 (mm) cc_final: 0.8333 (pp) REVERT: D 55 ASP cc_start: 0.8378 (t70) cc_final: 0.8006 (t70) REVERT: D 59 GLU cc_start: 0.8903 (pt0) cc_final: 0.8488 (pt0) REVERT: D 72 TYR cc_start: 0.8279 (t80) cc_final: 0.7898 (t80) REVERT: D 76 GLU cc_start: 0.8562 (mp0) cc_final: 0.8022 (mp0) REVERT: D 91 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8816 (ptpp) REVERT: D 112 GLN cc_start: 0.8256 (tt0) cc_final: 0.8022 (tt0) REVERT: D 116 MET cc_start: 0.8943 (ptp) cc_final: 0.8655 (ptp) REVERT: E 204 ARG cc_start: 0.8212 (ppt170) cc_final: 0.7941 (ppt170) REVERT: E 266 LYS cc_start: 0.8548 (mttt) cc_final: 0.8186 (mtmt) REVERT: E 273 ASP cc_start: 0.9349 (m-30) cc_final: 0.8805 (m-30) REVERT: E 277 TYR cc_start: 0.7913 (m-80) cc_final: 0.7640 (m-80) REVERT: F 221 GLN cc_start: 0.8871 (tp-100) cc_final: 0.7966 (tp-100) REVERT: F 225 MET cc_start: 0.8973 (mmt) cc_final: 0.8116 (mmm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2009 time to fit residues: 84.5795 Evaluate side-chains 246 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.0030 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 85 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.0060 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8918 Z= 0.198 Angle : 0.729 8.469 12045 Z= 0.369 Chirality : 0.045 0.329 1386 Planarity : 0.005 0.065 1497 Dihedral : 4.615 18.004 1162 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -0.29 (0.26), residues: 1077 helix: 0.73 (0.20), residues: 705 sheet: -2.23 (0.52), residues: 94 loop : -1.67 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP D 158 HIS 0.011 0.001 HIS E 285 PHE 0.026 0.001 PHE D 19 TYR 0.029 0.001 TYR E 277 ARG 0.014 0.001 ARG A 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8883 (tmm) cc_final: 0.7738 (tmm) REVERT: A 185 ARG cc_start: 0.8337 (tpt90) cc_final: 0.7788 (tpm170) REVERT: A 318 LEU cc_start: 0.9413 (tt) cc_final: 0.9200 (tt) REVERT: B 50 LYS cc_start: 0.8280 (pttt) cc_final: 0.8011 (ptmt) REVERT: B 152 MET cc_start: 0.8510 (mmm) cc_final: 0.8139 (mmm) REVERT: B 241 GLN cc_start: 0.7250 (pt0) cc_final: 0.6709 (pt0) REVERT: B 293 GLU cc_start: 0.7988 (pp20) cc_final: 0.7524 (tm-30) REVERT: C 21 CYS cc_start: 0.8097 (m) cc_final: 0.7873 (t) REVERT: C 49 MET cc_start: 0.9364 (ttp) cc_final: 0.9045 (ttp) REVERT: C 58 GLN cc_start: 0.8402 (pp30) cc_final: 0.7977 (tm-30) REVERT: D 49 MET cc_start: 0.8863 (mmp) cc_final: 0.8614 (mmm) REVERT: D 55 ASP cc_start: 0.8289 (t70) cc_final: 0.7898 (t70) REVERT: D 59 GLU cc_start: 0.8847 (pt0) cc_final: 0.8426 (pt0) REVERT: D 72 TYR cc_start: 0.8289 (t80) cc_final: 0.7771 (t80) REVERT: D 76 GLU cc_start: 0.8479 (mp0) cc_final: 0.7726 (mp0) REVERT: D 91 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8815 (ptpp) REVERT: D 112 GLN cc_start: 0.8256 (tt0) cc_final: 0.8036 (tt0) REVERT: D 116 MET cc_start: 0.8941 (ptp) cc_final: 0.8673 (ptp) REVERT: E 204 ARG cc_start: 0.8161 (ppt170) cc_final: 0.7921 (ppt170) REVERT: E 266 LYS cc_start: 0.8551 (mttt) cc_final: 0.8215 (mtmt) REVERT: E 273 ASP cc_start: 0.9298 (m-30) cc_final: 0.8704 (m-30) REVERT: E 274 LEU cc_start: 0.9002 (mm) cc_final: 0.8701 (mm) REVERT: E 277 TYR cc_start: 0.7732 (m-80) cc_final: 0.7532 (m-80) REVERT: F 221 GLN cc_start: 0.8825 (tp-100) cc_final: 0.7890 (tp-100) REVERT: F 225 MET cc_start: 0.8975 (mmt) cc_final: 0.8094 (mmm) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2059 time to fit residues: 90.2016 Evaluate side-chains 246 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.118279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085764 restraints weight = 27685.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088316 restraints weight = 16883.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.089939 restraints weight = 12223.829| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8918 Z= 0.242 Angle : 0.738 10.087 12045 Z= 0.379 Chirality : 0.045 0.328 1386 Planarity : 0.005 0.061 1497 Dihedral : 4.686 21.412 1162 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 1077 helix: 0.66 (0.19), residues: 705 sheet: -2.27 (0.52), residues: 92 loop : -1.63 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.003 TRP D 158 HIS 0.007 0.001 HIS A 296 PHE 0.028 0.002 PHE D 19 TYR 0.036 0.001 TYR E 277 ARG 0.014 0.001 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.72 seconds wall clock time: 43 minutes 48.20 seconds (2628.20 seconds total)