Starting phenix.real_space_refine on Thu Mar 14 15:02:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/03_2024/8jii_36312_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/03_2024/8jii_36312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/03_2024/8jii_36312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/03_2024/8jii_36312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/03_2024/8jii_36312_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/03_2024/8jii_36312_neut_updated.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 sd= 0.132 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 69 5.16 5 C 5806 2.51 5 N 1543 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 270": "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: 9083 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'IX8': 1, 'NIO': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 5.54, per 1000 atoms: 0.61 Number of scatterers: 9083 At special positions: 0 Unit cell: (93.5, 119.85, 135.15, 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 69 16.00 O 1665 8.00 N 1543 7.00 C 5806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.04 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: 3.31 Conformation dependent library (CDL) restraints added in 1.9 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 27.6% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 8 through 22 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'D' and resid 11 through 25 Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 212 through 214 No H-bonds generated for 'chain 'D' and resid 212 through 214' Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 271 through 280 removed outlier: 3.527A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 4.019A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 350 removed outlier: 3.654A pdb=" N ASP D 350 " --> pdb=" O ASN D 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'A' and resid 26 through 51 Proline residue: A 31 - end of helix removed outlier: 3.876A pdb=" N GLY A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 75 through 78 No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 102 removed outlier: 3.776A pdb=" N CYS A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 112 through 115 No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 121 through 130 removed outlier: 4.323A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.516A pdb=" N GLY A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 189 through 214 removed outlier: 3.574A pdb=" N GLU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.998A pdb=" N PHE A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.962A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.741A pdb=" N VAL A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 289 removed outlier: 4.402A pdb=" N SER A 271 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU A 280 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 284 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 287 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.011A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.796A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.647A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.817A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.868A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.690A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.789A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 319 through 323 removed outlier: 6.472A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.737A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.188A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 226 through 231 removed outlier: 6.233A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 828 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: 2.75 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 1275 1.25 - 1.39: 2517 1.39 - 1.53: 5075 1.53 - 1.68: 316 1.68 - 1.82: 100 Bond restraints: 9283 Sorted by residual: bond pdb=" C9 IX8 A 403 " pdb=" N10 IX8 A 403 " ideal model delta sigma weight residual 1.386 1.266 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C27 IX8 A 403 " pdb=" C32 IX8 A 403 " ideal model delta sigma weight residual 1.396 1.277 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C4 IX8 A 403 " pdb=" O5 IX8 A 403 " ideal model delta sigma weight residual 1.221 1.104 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C2 IX8 A 403 " pdb=" C25 IX8 A 403 " ideal model delta sigma weight residual 1.522 1.428 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C27 IX8 A 403 " pdb=" C28 IX8 A 403 " ideal model delta sigma weight residual 1.393 1.302 0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 9278 not shown) Histogram of bond angle deviations from ideal: 95.43 - 103.15: 62 103.15 - 110.88: 3190 110.88 - 118.60: 4060 118.60 - 126.32: 5098 126.32 - 134.04: 154 Bond angle restraints: 12564 Sorted by residual: angle pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" C VAL A 123 " ideal model delta sigma weight residual 111.90 106.74 5.16 8.10e-01 1.52e+00 4.06e+01 angle pdb=" N ILE A 77 " pdb=" CA ILE A 77 " pdb=" C ILE A 77 " ideal model delta sigma weight residual 111.62 106.70 4.92 7.90e-01 1.60e+00 3.88e+01 angle pdb=" C6 IX8 A 403 " pdb=" C4 IX8 A 403 " pdb=" N3 IX8 A 403 " ideal model delta sigma weight residual 114.73 132.05 -17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 131.62 -10.08 1.91e+00 2.74e-01 2.78e+01 angle pdb=" C23 IX8 A 403 " pdb=" C22 IX8 A 403 " pdb=" C24 IX8 A 403 " ideal model delta sigma weight residual 110.88 95.43 15.45 3.00e+00 1.11e-01 2.65e+01 ... (remaining 12559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4983 17.89 - 35.79: 470 35.79 - 53.68: 75 53.68 - 71.57: 14 71.57 - 89.46: 5 Dihedral angle restraints: 5547 sinusoidal: 2235 harmonic: 3312 Sorted by residual: dihedral pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" N PHE A 240 " pdb=" CA PHE A 240 " ideal model delta harmonic sigma weight residual 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASP A 14 " pdb=" C ASP A 14 " pdb=" N LYS A 15 " pdb=" CA LYS A 15 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C SER A 179 " pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" CB SER A 179 " ideal model delta harmonic sigma weight residual -122.60 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 5544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1010 0.047 - 0.093: 310 0.093 - 0.140: 80 0.140 - 0.186: 5 0.186 - 0.233: 3 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA GLU D 298 " pdb=" N GLU D 298 " pdb=" C GLU D 298 " pdb=" CB GLU D 298 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA CYS A 177 " pdb=" N CYS A 177 " pdb=" C CYS A 177 " pdb=" CB CYS A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA SER A 178 " pdb=" N SER A 178 " pdb=" C SER A 178 " pdb=" CB SER A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1405 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 IX8 A 403 " 0.015 2.00e-02 2.50e+03 3.10e-02 1.20e+01 pdb=" C4 IX8 A 403 " -0.060 2.00e-02 2.50e+03 pdb=" C6 IX8 A 403 " 0.029 2.00e-02 2.50e+03 pdb=" N3 IX8 A 403 " 0.002 2.00e-02 2.50e+03 pdb=" O5 IX8 A 403 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 118 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" CG ASP B 118 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP B 118 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 118 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO S 75 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.032 5.00e-02 4.00e+02 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 56 2.55 - 3.14: 6784 3.14 - 3.73: 12731 3.73 - 4.31: 18236 4.31 - 4.90: 32049 Nonbonded interactions: 69856 Sorted by model distance: nonbonded pdb=" O SER D 293 " pdb=" OD1 ASN D 294 " model vdw 1.963 3.040 nonbonded pdb=" NE2 GLN D 304 " pdb=" OE2 GLU D 308 " model vdw 2.197 2.520 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.269 2.440 nonbonded pdb=" OG SER A 62 " pdb=" OD2 ASP A 124 " model vdw 2.283 2.440 nonbonded pdb=" OE2 GLU D 8 " pdb=" OH TYR S 175 " model vdw 2.294 2.440 ... (remaining 69851 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: 0.870 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: 4.000 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.910 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.006 0.120 9283 Z= 0.408 Angle : 0.837 17.321 12564 Z= 0.453 Chirality : 0.047 0.233 1408 Planarity : 0.004 0.058 1581 Dihedral : 14.119 89.464 3395 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.24), residues: 1130 helix: -0.86 (0.29), residues: 325 sheet: -0.58 (0.29), residues: 301 loop : -2.01 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP S 47 HIS 0.011 0.001 HIS A 223 PHE 0.015 0.002 PHE B 234 TYR 0.028 0.002 TYR A 87 ARG 0.008 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.6785 (ttp) cc_final: 0.6464 (ttm) REVERT: D 9 ASP cc_start: 0.7642 (m-30) cc_final: 0.7297 (m-30) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2527 time to fit residues: 41.8844 Evaluate side-chains 109 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9283 Z= 0.171 Angle : 0.573 7.000 12564 Z= 0.295 Chirality : 0.042 0.137 1408 Planarity : 0.004 0.049 1581 Dihedral : 6.292 78.378 1321 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.61 % Allowed : 6.09 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.54 (0.24), residues: 1130 helix: -0.56 (0.30), residues: 336 sheet: -0.26 (0.30), residues: 299 loop : -1.79 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 234 TYR 0.018 0.001 TYR A 87 ARG 0.002 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.049 Fit side-chains REVERT: B 262 MET cc_start: 0.6671 (ttp) cc_final: 0.6423 (ttm) REVERT: C 21 MET cc_start: 0.6679 (tmm) cc_final: 0.5556 (tmm) REVERT: D 9 ASP cc_start: 0.7633 (m-30) cc_final: 0.7288 (m-30) REVERT: D 32 ARG cc_start: 0.8199 (ptp-110) cc_final: 0.7824 (mtm110) REVERT: A 39 ILE cc_start: 0.8537 (tp) cc_final: 0.8158 (tp) REVERT: A 40 PHE cc_start: 0.7847 (m-10) cc_final: 0.7611 (m-10) outliers start: 6 outliers final: 6 residues processed: 115 average time/residue: 0.2617 time to fit residues: 39.7032 Evaluate side-chains 112 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9283 Z= 0.190 Angle : 0.552 7.349 12564 Z= 0.288 Chirality : 0.042 0.157 1408 Planarity : 0.003 0.047 1581 Dihedral : 6.081 79.279 1321 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.91 % Allowed : 10.04 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.34 (0.25), residues: 1130 helix: -0.30 (0.30), residues: 336 sheet: -0.16 (0.30), residues: 299 loop : -1.73 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 47 HIS 0.006 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR S 190 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.087 Fit side-chains REVERT: B 262 MET cc_start: 0.6682 (ttp) cc_final: 0.6419 (ttm) REVERT: D 9 ASP cc_start: 0.7657 (m-30) cc_final: 0.7324 (m-30) REVERT: D 248 LYS cc_start: 0.7063 (mptt) cc_final: 0.6789 (mmtt) REVERT: A 39 ILE cc_start: 0.8594 (tp) cc_final: 0.8216 (tp) REVERT: A 40 PHE cc_start: 0.7761 (m-80) cc_final: 0.7475 (m-10) REVERT: A 166 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7707 (tttm) outliers start: 9 outliers final: 7 residues processed: 129 average time/residue: 0.2695 time to fit residues: 45.3980 Evaluate side-chains 125 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0010 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9283 Z= 0.120 Angle : 0.492 7.258 12564 Z= 0.257 Chirality : 0.041 0.132 1408 Planarity : 0.003 0.045 1581 Dihedral : 5.750 74.750 1321 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.22 % Allowed : 11.76 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.11 (0.25), residues: 1130 helix: -0.01 (0.31), residues: 332 sheet: -0.04 (0.30), residues: 298 loop : -1.65 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR S 190 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: D 9 ASP cc_start: 0.7605 (m-30) cc_final: 0.7284 (m-30) REVERT: D 32 ARG cc_start: 0.8121 (ptp-110) cc_final: 0.7793 (mtm110) REVERT: A 39 ILE cc_start: 0.8581 (tp) cc_final: 0.8188 (tp) REVERT: A 40 PHE cc_start: 0.7763 (m-80) cc_final: 0.7461 (m-10) REVERT: A 92 ASP cc_start: 0.7461 (t0) cc_final: 0.7085 (t0) REVERT: A 166 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7521 (tttm) outliers start: 12 outliers final: 7 residues processed: 127 average time/residue: 0.2703 time to fit residues: 44.8940 Evaluate side-chains 121 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 227 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 0.0060 chunk 92 optimal weight: 0.0970 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN A 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9283 Z= 0.334 Angle : 0.617 9.148 12564 Z= 0.321 Chirality : 0.045 0.138 1408 Planarity : 0.004 0.047 1581 Dihedral : 6.104 80.647 1321 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.43 % Allowed : 11.76 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.31 (0.25), residues: 1130 helix: -0.21 (0.30), residues: 335 sheet: -0.16 (0.30), residues: 302 loop : -1.76 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 47 HIS 0.009 0.001 HIS S 35 PHE 0.017 0.002 PHE S 29 TYR 0.014 0.002 TYR S 190 ARG 0.005 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.029 Fit side-chains REVERT: D 9 ASP cc_start: 0.7667 (m-30) cc_final: 0.7317 (m-30) REVERT: D 248 LYS cc_start: 0.7082 (mptt) cc_final: 0.6787 (mmtt) REVERT: S 177 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.6557 (p90) REVERT: A 166 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7473 (tttm) outliers start: 24 outliers final: 14 residues processed: 131 average time/residue: 0.2638 time to fit residues: 45.3661 Evaluate side-chains 127 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9283 Z= 0.204 Angle : 0.551 9.250 12564 Z= 0.286 Chirality : 0.042 0.135 1408 Planarity : 0.003 0.045 1581 Dihedral : 5.991 78.408 1321 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.93 % Allowed : 12.68 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.22 (0.25), residues: 1130 helix: -0.16 (0.30), residues: 335 sheet: -0.06 (0.30), residues: 299 loop : -1.72 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.006 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR S 190 ARG 0.004 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.011 Fit side-chains REVERT: D 9 ASP cc_start: 0.7634 (m-30) cc_final: 0.7300 (m-30) REVERT: D 248 LYS cc_start: 0.7050 (mptt) cc_final: 0.6748 (mmtt) REVERT: A 102 LEU cc_start: 0.8101 (mm) cc_final: 0.7897 (mt) REVERT: A 166 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7466 (tttm) REVERT: A 199 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7248 (mp) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 0.2818 time to fit residues: 46.5298 Evaluate side-chains 126 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0010 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 0.0000 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.0370 overall best weight: 0.4068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9283 Z= 0.124 Angle : 0.500 10.791 12564 Z= 0.259 Chirality : 0.040 0.130 1408 Planarity : 0.003 0.043 1581 Dihedral : 5.692 73.490 1321 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.93 % Allowed : 13.29 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.01 (0.25), residues: 1130 helix: 0.07 (0.31), residues: 331 sheet: 0.05 (0.30), residues: 296 loop : -1.61 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR S 190 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: C 21 MET cc_start: 0.6817 (tmm) cc_final: 0.5434 (tmm) REVERT: D 9 ASP cc_start: 0.7603 (m-30) cc_final: 0.7267 (m-30) REVERT: D 24 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7434 (ttm170) REVERT: D 26 ASP cc_start: 0.7571 (t0) cc_final: 0.7184 (m-30) REVERT: S 177 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.5962 (p90) REVERT: A 166 LYS cc_start: 0.7805 (ttmm) cc_final: 0.7517 (tttm) outliers start: 19 outliers final: 11 residues processed: 133 average time/residue: 0.2660 time to fit residues: 46.4426 Evaluate side-chains 131 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 227 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9283 Z= 0.149 Angle : 0.510 9.680 12564 Z= 0.264 Chirality : 0.041 0.129 1408 Planarity : 0.003 0.044 1581 Dihedral : 5.640 73.281 1321 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.83 % Allowed : 13.79 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.93 (0.25), residues: 1130 helix: 0.10 (0.31), residues: 333 sheet: 0.18 (0.30), residues: 294 loop : -1.59 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR S 190 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: C 21 MET cc_start: 0.6733 (tmm) cc_final: 0.5399 (tmm) REVERT: D 9 ASP cc_start: 0.7605 (m-30) cc_final: 0.7273 (m-30) REVERT: D 26 ASP cc_start: 0.7523 (t0) cc_final: 0.7114 (m-30) REVERT: S 177 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6047 (p90) REVERT: A 166 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7399 (tttm) outliers start: 18 outliers final: 13 residues processed: 129 average time/residue: 0.2653 time to fit residues: 44.9618 Evaluate side-chains 129 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 227 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9283 Z= 0.166 Angle : 0.519 9.445 12564 Z= 0.268 Chirality : 0.041 0.131 1408 Planarity : 0.003 0.044 1581 Dihedral : 5.644 73.475 1321 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.72 % Allowed : 14.40 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.92 (0.25), residues: 1130 helix: 0.12 (0.30), residues: 334 sheet: 0.17 (0.30), residues: 298 loop : -1.59 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.013 0.001 TYR S 190 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: C 21 MET cc_start: 0.6728 (tmm) cc_final: 0.5420 (tmm) REVERT: D 9 ASP cc_start: 0.7611 (m-30) cc_final: 0.7281 (m-30) REVERT: D 26 ASP cc_start: 0.7510 (t0) cc_final: 0.7095 (m-30) REVERT: S 177 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6059 (p90) REVERT: A 84 MET cc_start: 0.6710 (tpp) cc_final: 0.5962 (ttt) REVERT: A 166 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7426 (tttm) outliers start: 17 outliers final: 14 residues processed: 127 average time/residue: 0.2720 time to fit residues: 45.4091 Evaluate side-chains 133 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 227 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9283 Z= 0.337 Angle : 0.633 9.863 12564 Z= 0.325 Chirality : 0.045 0.139 1408 Planarity : 0.004 0.046 1581 Dihedral : 6.087 78.925 1321 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.62 % Allowed : 14.50 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1130 helix: -0.06 (0.30), residues: 334 sheet: -0.02 (0.30), residues: 302 loop : -1.70 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.009 0.001 HIS S 35 PHE 0.017 0.002 PHE S 29 TYR 0.014 0.002 TYR S 190 ARG 0.004 0.000 ARG A 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.947 Fit side-chains REVERT: B 124 TYR cc_start: 0.8537 (m-80) cc_final: 0.8314 (m-80) REVERT: B 234 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: C 21 MET cc_start: 0.6717 (tmm) cc_final: 0.5438 (tmm) REVERT: D 9 ASP cc_start: 0.7653 (m-30) cc_final: 0.7322 (m-30) REVERT: D 26 ASP cc_start: 0.7531 (t0) cc_final: 0.7144 (m-30) REVERT: S 177 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.6572 (p90) REVERT: A 84 MET cc_start: 0.6737 (tpp) cc_final: 0.5979 (ttt) REVERT: A 166 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7848 (tttm) REVERT: A 290 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6888 (t0) outliers start: 16 outliers final: 13 residues processed: 129 average time/residue: 0.2730 time to fit residues: 46.0324 Evaluate side-chains 133 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134081 restraints weight = 12822.839| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.74 r_work: 0.3513 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9283 Z= 0.155 Angle : 0.530 9.299 12564 Z= 0.276 Chirality : 0.041 0.147 1408 Planarity : 0.003 0.044 1581 Dihedral : 5.836 75.039 1321 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.62 % Allowed : 14.60 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.98 (0.25), residues: 1130 helix: 0.08 (0.30), residues: 334 sheet: 0.13 (0.30), residues: 297 loop : -1.62 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.014 0.001 TYR S 190 ARG 0.003 0.000 ARG D 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.10 seconds wall clock time: 40 minutes 54.49 seconds (2454.49 seconds total)