Starting phenix.real_space_refine on Thu Mar 14 15:32:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/03_2024/6omm_20126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/03_2024/6omm_20126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/03_2024/6omm_20126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/03_2024/6omm_20126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/03_2024/6omm_20126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omm_20126/03_2024/6omm_20126_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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5907 2.51 5 N 1510 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 26": "NH1" <-> "NH2" Residue "R ARG 54": "NH1" <-> "NH2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "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: 9134 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2341 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 59 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1754 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 194 Unusual residues: {'CLR': 5, 'PLM': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 5.37, per 1000 atoms: 0.59 Number of scatterers: 9134 At special positions: 0 Unit cell: (122.451, 89.523, 128.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1652 8.00 N 1510 7.00 C 5907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QXV L 9 " Number of C-beta restraints generated: 2120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 34.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'R' and resid 22 through 49 Proline residue: R 29 - end of helix removed outlier: 3.665A pdb=" N VAL R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 76 removed outlier: 3.705A pdb=" N SER R 73 " --> pdb=" O LEU R 69 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 95 through 128 removed outlier: 3.702A pdb=" N LYS R 99 " --> pdb=" O TRP R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 139 through 156 removed outlier: 4.188A pdb=" N VAL R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 158 through 163 removed outlier: 4.242A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 184 No H-bonds generated for 'chain 'R' and resid 181 through 184' Processing helix chain 'R' and resid 187 through 209 removed outlier: 4.237A pdb=" N LYS R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE R 208 " --> pdb=" O ILE R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 231 removed outlier: 3.712A pdb=" N SER R 215 " --> pdb=" O SER R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 272 removed outlier: 3.707A pdb=" N VAL R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE R 252 " --> pdb=" O ALA R 248 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP R 254 " --> pdb=" O PHE R 250 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE R 255 " --> pdb=" O PHE R 251 " (cutoff:3.500A) Proline residue: R 256 - end of helix removed outlier: 3.595A pdb=" N VAL R 260 " --> pdb=" O PRO R 256 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS R 269 " --> pdb=" O THR R 265 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLU R 270 " --> pdb=" O VAL R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 282 No H-bonds generated for 'chain 'R' and resid 279 through 282' Processing helix chain 'R' and resid 284 through 302 removed outlier: 3.583A pdb=" N ASN R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 316 Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.540A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.474A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.521A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 320 through 323 removed outlier: 3.801A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.042A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.157A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.979A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.607A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.752A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.733A 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: 7.087A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.567A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.735A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.533A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.669A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.044A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1125 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: 2.52 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2798 1.34 - 1.46: 2015 1.46 - 1.58: 4429 1.58 - 1.70: 1 1.70 - 1.82: 96 Bond restraints: 9339 Sorted by residual: bond pdb=" C QXV L 9 " pdb=" NXT QXV L 9 " ideal model delta sigma weight residual 1.339 1.444 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CG LEU B 336 " pdb=" CD2 LEU B 336 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CG LEU B 70 " pdb=" CD2 LEU B 70 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CG LEU B 336 " pdb=" CD1 LEU B 336 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.19e+00 bond pdb=" C LEU R 162 " pdb=" N PHE R 163 " ideal model delta sigma weight residual 1.334 1.369 -0.034 1.43e-02 4.89e+03 5.77e+00 ... (remaining 9334 not shown) Histogram of bond angle deviations from ideal: 96.14 - 103.74: 117 103.74 - 111.33: 3818 111.33 - 118.92: 3762 118.92 - 126.51: 4813 126.51 - 134.11: 152 Bond angle restraints: 12662 Sorted by residual: angle pdb=" N VAL R 160 " pdb=" CA VAL R 160 " pdb=" C VAL R 160 " ideal model delta sigma weight residual 110.72 116.43 -5.71 1.01e+00 9.80e-01 3.20e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.35 127.61 -5.26 1.46e+00 4.69e-01 1.30e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.00e+00 1.00e+00 1.21e+01 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 5426 15.10 - 30.20: 247 30.20 - 45.30: 80 45.30 - 60.40: 1 60.40 - 75.50: 4 Dihedral angle restraints: 5758 sinusoidal: 2468 harmonic: 3290 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -121.33 35.33 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CA HIS E 35 " pdb=" C HIS E 35 " pdb=" N TRP E 36 " pdb=" CA TRP E 36 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1298 0.096 - 0.192: 135 0.192 - 0.288: 7 0.288 - 0.384: 6 0.384 - 0.480: 4 Chirality restraints: 1450 Sorted by residual: chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C15 CLR R 404 " pdb=" C8 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1447 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 158 " 0.016 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C LEU R 158 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU R 158 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO R 159 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " 0.018 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP E 111 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 27 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ILE R 27 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE R 27 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU R 28 " 0.013 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 918 2.76 - 3.29: 8580 3.29 - 3.83: 15249 3.83 - 4.36: 17857 4.36 - 4.90: 31056 Nonbonded interactions: 73660 Sorted by model distance: nonbonded pdb=" O ALA R 153 " pdb=" OG1 THR R 157 " model vdw 2.222 2.440 nonbonded pdb=" OG SER B 281 " pdb=" O HIS C 44 " model vdw 2.279 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.352 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.357 2.440 ... (remaining 73655 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.140 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.970 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 9339 Z= 0.342 Angle : 0.928 9.207 12662 Z= 0.483 Chirality : 0.064 0.480 1450 Planarity : 0.006 0.048 1555 Dihedral : 9.848 75.504 3629 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.21), residues: 1123 helix: -1.84 (0.20), residues: 410 sheet: -1.61 (0.29), residues: 273 loop : -2.06 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP E 111 HIS 0.008 0.002 HIS E 35 PHE 0.033 0.003 PHE R 161 TYR 0.021 0.002 TYR E 59 ARG 0.015 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 39 LEU cc_start: 0.8789 (tt) cc_final: 0.8500 (tt) REVERT: R 90 LYS cc_start: 0.7884 (mttt) cc_final: 0.6884 (mmmt) REVERT: R 174 THR cc_start: 0.6256 (p) cc_final: 0.5610 (p) REVERT: R 179 ASN cc_start: 0.7691 (t0) cc_final: 0.7161 (m110) REVERT: R 191 LEU cc_start: 0.6671 (tp) cc_final: 0.6432 (pp) REVERT: R 300 MET cc_start: 0.8486 (mtt) cc_final: 0.8215 (mtm) REVERT: A 48 THR cc_start: 0.8560 (m) cc_final: 0.8289 (p) REVERT: A 327 THR cc_start: 0.8168 (p) cc_final: 0.7403 (m) REVERT: A 346 ASN cc_start: 0.8778 (m-40) cc_final: 0.8513 (m110) REVERT: B 267 ASP cc_start: 0.8710 (m-30) cc_final: 0.8263 (t0) REVERT: B 273 ILE cc_start: 0.8378 (mp) cc_final: 0.8163 (mt) REVERT: B 291 ASP cc_start: 0.7792 (t70) cc_final: 0.7490 (t70) REVERT: B 297 TRP cc_start: 0.8763 (m100) cc_final: 0.8362 (m100) REVERT: E 217 SER cc_start: 0.8144 (t) cc_final: 0.6768 (p) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2466 time to fit residues: 104.6326 Evaluate side-chains 203 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 258 GLN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 GLN A 204 GLN B 32 GLN B 62 HIS B 88 ASN B 91 HIS B 175 GLN E 13 GLN E 142 GLN E 194 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9339 Z= 0.216 Angle : 0.581 7.858 12662 Z= 0.296 Chirality : 0.041 0.146 1450 Planarity : 0.004 0.037 1555 Dihedral : 6.019 55.072 1596 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.87 % Favored : 98.04 % Rotamer: Outliers : 2.87 % Allowed : 11.99 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.23), residues: 1123 helix: 0.09 (0.25), residues: 411 sheet: -1.18 (0.30), residues: 266 loop : -1.66 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.017 0.001 PHE R 96 TYR 0.014 0.001 TYR B 59 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.7162 (mtp85) REVERT: R 90 LYS cc_start: 0.8021 (mttt) cc_final: 0.7715 (mmmm) REVERT: R 191 LEU cc_start: 0.6962 (tp) cc_final: 0.6600 (pp) REVERT: R 269 LYS cc_start: 0.8221 (mptt) cc_final: 0.7905 (mtpt) REVERT: R 270 GLU cc_start: 0.7558 (mp0) cc_final: 0.7334 (tp30) REVERT: R 300 MET cc_start: 0.8748 (mtt) cc_final: 0.8510 (mtm) REVERT: A 48 THR cc_start: 0.8558 (m) cc_final: 0.8336 (p) REVERT: A 52 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6211 (tt0) REVERT: A 327 THR cc_start: 0.7784 (p) cc_final: 0.7272 (m) REVERT: A 331 ASN cc_start: 0.8101 (m-40) cc_final: 0.7784 (m110) REVERT: A 346 ASN cc_start: 0.8858 (m-40) cc_final: 0.8578 (m110) REVERT: B 10 GLU cc_start: 0.8062 (tp30) cc_final: 0.7845 (tp30) REVERT: B 267 ASP cc_start: 0.8771 (m-30) cc_final: 0.8331 (t0) REVERT: B 273 ILE cc_start: 0.8384 (mp) cc_final: 0.8122 (mt) REVERT: B 291 ASP cc_start: 0.8076 (t70) cc_final: 0.7773 (t70) REVERT: B 297 TRP cc_start: 0.8779 (m100) cc_final: 0.8287 (m100) REVERT: C 13 ARG cc_start: 0.7887 (ptp-110) cc_final: 0.7519 (ttm-80) REVERT: E 6 GLU cc_start: 0.8219 (mp0) cc_final: 0.7374 (mp0) REVERT: E 220 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7874 (mp0) outliers start: 28 outliers final: 14 residues processed: 230 average time/residue: 0.2339 time to fit residues: 72.3355 Evaluate side-chains 200 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 175 GLN E 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9339 Z= 0.200 Angle : 0.548 8.769 12662 Z= 0.280 Chirality : 0.041 0.202 1450 Planarity : 0.003 0.038 1555 Dihedral : 5.702 54.894 1596 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.79 % Allowed : 13.01 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1123 helix: 0.75 (0.26), residues: 413 sheet: -0.84 (0.30), residues: 260 loop : -1.50 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 102 PHE 0.011 0.001 PHE R 96 TYR 0.012 0.001 TYR B 59 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.7148 (mtp85) REVERT: R 44 ASN cc_start: 0.8288 (m-40) cc_final: 0.7556 (m110) REVERT: R 71 ASP cc_start: 0.8124 (t70) cc_final: 0.7659 (t70) REVERT: R 90 LYS cc_start: 0.8313 (mttt) cc_final: 0.7917 (mmmm) REVERT: R 191 LEU cc_start: 0.6914 (tp) cc_final: 0.6622 (pp) REVERT: R 269 LYS cc_start: 0.8141 (mptt) cc_final: 0.7850 (mtpt) REVERT: R 270 GLU cc_start: 0.7646 (mp0) cc_final: 0.7306 (tp30) REVERT: R 300 MET cc_start: 0.8760 (mtt) cc_final: 0.8475 (mtm) REVERT: A 48 THR cc_start: 0.8548 (m) cc_final: 0.8327 (p) REVERT: A 52 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: A 242 ARG cc_start: 0.7526 (mtt-85) cc_final: 0.7314 (mtt-85) REVERT: A 327 THR cc_start: 0.7908 (p) cc_final: 0.7592 (m) REVERT: A 331 ASN cc_start: 0.8089 (m-40) cc_final: 0.7861 (m110) REVERT: B 10 GLU cc_start: 0.8115 (tp30) cc_final: 0.7811 (tp30) REVERT: B 175 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8470 (pp30) REVERT: B 267 ASP cc_start: 0.8800 (m-30) cc_final: 0.8264 (t0) REVERT: B 273 ILE cc_start: 0.8373 (mp) cc_final: 0.8123 (mt) REVERT: B 291 ASP cc_start: 0.8133 (t70) cc_final: 0.7756 (t70) REVERT: C 13 ARG cc_start: 0.7988 (ptp-110) cc_final: 0.7591 (ttm-80) REVERT: C 37 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8492 (tt) REVERT: E 6 GLU cc_start: 0.8319 (mp0) cc_final: 0.7674 (mp0) REVERT: E 153 GLU cc_start: 0.8200 (pt0) cc_final: 0.7925 (pm20) REVERT: E 220 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7946 (mp0) outliers start: 37 outliers final: 23 residues processed: 223 average time/residue: 0.2073 time to fit residues: 62.3200 Evaluate side-chains 208 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 9339 Z= 0.376 Angle : 0.641 8.206 12662 Z= 0.325 Chirality : 0.044 0.162 1450 Planarity : 0.004 0.041 1555 Dihedral : 6.041 55.305 1596 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.10 % Allowed : 14.34 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1123 helix: 0.91 (0.26), residues: 413 sheet: -0.83 (0.28), residues: 288 loop : -1.42 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 95 HIS 0.007 0.002 HIS B 142 PHE 0.011 0.002 PHE B 278 TYR 0.016 0.002 TYR B 59 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.308 Fit side-chains REVERT: R 90 LYS cc_start: 0.8348 (mttt) cc_final: 0.7961 (mmmm) REVERT: R 191 LEU cc_start: 0.7137 (tp) cc_final: 0.6734 (pp) REVERT: R 269 LYS cc_start: 0.8110 (mptt) cc_final: 0.7793 (mtpt) REVERT: R 270 GLU cc_start: 0.7689 (mp0) cc_final: 0.7384 (tp30) REVERT: R 300 MET cc_start: 0.8849 (mtt) cc_final: 0.8557 (mtm) REVERT: A 48 THR cc_start: 0.8600 (m) cc_final: 0.8359 (p) REVERT: A 52 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: A 327 THR cc_start: 0.7897 (p) cc_final: 0.7604 (m) REVERT: A 331 ASN cc_start: 0.8209 (m-40) cc_final: 0.7948 (m110) REVERT: B 10 GLU cc_start: 0.8133 (tp30) cc_final: 0.7806 (tp30) REVERT: B 219 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8479 (mtt-85) REVERT: B 243 THR cc_start: 0.8790 (m) cc_final: 0.8462 (p) REVERT: B 267 ASP cc_start: 0.8886 (m-30) cc_final: 0.8478 (t0) REVERT: B 291 ASP cc_start: 0.8348 (t70) cc_final: 0.7996 (t70) REVERT: C 13 ARG cc_start: 0.8187 (ptp-110) cc_final: 0.7756 (ttm-80) REVERT: E 140 MET cc_start: 0.8988 (mmm) cc_final: 0.8272 (mmm) outliers start: 40 outliers final: 27 residues processed: 216 average time/residue: 0.2328 time to fit residues: 67.9675 Evaluate side-chains 201 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9339 Z= 0.249 Angle : 0.565 7.595 12662 Z= 0.288 Chirality : 0.041 0.141 1450 Planarity : 0.003 0.043 1555 Dihedral : 5.596 54.184 1596 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.59 % Allowed : 15.88 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1123 helix: 0.96 (0.26), residues: 423 sheet: -0.80 (0.28), residues: 288 loop : -1.26 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 95 HIS 0.005 0.001 HIS R 102 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR B 59 ARG 0.003 0.000 ARG R 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: R 90 LYS cc_start: 0.8218 (mttt) cc_final: 0.7842 (mmmm) REVERT: R 161 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8037 (t80) REVERT: R 191 LEU cc_start: 0.7097 (tp) cc_final: 0.6706 (pp) REVERT: R 269 LYS cc_start: 0.8120 (mptt) cc_final: 0.7825 (mtpt) REVERT: R 270 GLU cc_start: 0.7644 (mp0) cc_final: 0.7335 (tp30) REVERT: R 300 MET cc_start: 0.8896 (mtt) cc_final: 0.8557 (mtm) REVERT: A 48 THR cc_start: 0.8517 (m) cc_final: 0.8273 (p) REVERT: A 52 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6697 (tt0) REVERT: A 242 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7627 (mtt-85) REVERT: A 287 TYR cc_start: 0.7115 (m-80) cc_final: 0.6887 (m-10) REVERT: A 331 ASN cc_start: 0.8147 (m-40) cc_final: 0.7869 (m-40) REVERT: B 10 GLU cc_start: 0.8126 (tp30) cc_final: 0.7819 (tp30) REVERT: B 172 GLU cc_start: 0.8414 (pm20) cc_final: 0.8163 (pm20) REVERT: B 243 THR cc_start: 0.8685 (m) cc_final: 0.8339 (p) REVERT: B 267 ASP cc_start: 0.8897 (m-30) cc_final: 0.8469 (t0) REVERT: B 273 ILE cc_start: 0.8581 (mp) cc_final: 0.8161 (mt) REVERT: B 291 ASP cc_start: 0.8229 (t70) cc_final: 0.7887 (t70) REVERT: B 297 TRP cc_start: 0.8768 (m100) cc_final: 0.8198 (m100) REVERT: C 13 ARG cc_start: 0.8151 (ptp-110) cc_final: 0.7730 (ttm-80) REVERT: C 16 VAL cc_start: 0.9155 (t) cc_final: 0.8791 (m) REVERT: E 140 MET cc_start: 0.9070 (mmm) cc_final: 0.8266 (mmm) REVERT: E 153 GLU cc_start: 0.8099 (pt0) cc_final: 0.7755 (pm20) outliers start: 35 outliers final: 27 residues processed: 207 average time/residue: 0.2279 time to fit residues: 63.7158 Evaluate side-chains 204 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 175 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.0060 chunk 56 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9339 Z= 0.191 Angle : 0.550 9.062 12662 Z= 0.278 Chirality : 0.040 0.144 1450 Planarity : 0.003 0.043 1555 Dihedral : 5.210 55.153 1596 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.79 % Allowed : 16.39 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1123 helix: 1.20 (0.26), residues: 423 sheet: -0.55 (0.29), residues: 274 loop : -1.23 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.014 0.001 TYR A 296 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7386 (ttp-110) cc_final: 0.6821 (mtm110) REVERT: R 39 LEU cc_start: 0.9160 (tp) cc_final: 0.8766 (tt) REVERT: R 90 LYS cc_start: 0.8175 (mttt) cc_final: 0.7840 (mmmm) REVERT: R 91 TRP cc_start: 0.8198 (t-100) cc_final: 0.7856 (t-100) REVERT: R 161 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8130 (t80) REVERT: R 191 LEU cc_start: 0.6962 (tp) cc_final: 0.6643 (pp) REVERT: R 269 LYS cc_start: 0.8022 (mptt) cc_final: 0.7699 (mtpt) REVERT: R 270 GLU cc_start: 0.7789 (mp0) cc_final: 0.7271 (tp30) REVERT: R 274 TYR cc_start: 0.7944 (m-80) cc_final: 0.7591 (m-10) REVERT: R 300 MET cc_start: 0.8875 (mtt) cc_final: 0.8527 (mtm) REVERT: A 48 THR cc_start: 0.8329 (m) cc_final: 0.8057 (p) REVERT: A 331 ASN cc_start: 0.8118 (m-40) cc_final: 0.7854 (m110) REVERT: B 10 GLU cc_start: 0.8137 (tp30) cc_final: 0.7796 (tp30) REVERT: B 15 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8371 (mtpp) REVERT: B 170 ASP cc_start: 0.8870 (t0) cc_final: 0.8483 (t0) REVERT: B 217 MET cc_start: 0.7640 (ppp) cc_final: 0.7405 (ppp) REVERT: B 234 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8963 (m-80) REVERT: B 243 THR cc_start: 0.8639 (m) cc_final: 0.8313 (p) REVERT: B 267 ASP cc_start: 0.8838 (m-30) cc_final: 0.8420 (t0) REVERT: B 273 ILE cc_start: 0.8492 (mp) cc_final: 0.8062 (mt) REVERT: B 291 ASP cc_start: 0.8136 (t70) cc_final: 0.7789 (t70) REVERT: C 13 ARG cc_start: 0.8115 (ptp-110) cc_final: 0.7722 (ttm-80) REVERT: E 140 MET cc_start: 0.9048 (mmm) cc_final: 0.8279 (mmm) REVERT: E 220 GLU cc_start: 0.7899 (mp0) cc_final: 0.7671 (mp0) outliers start: 37 outliers final: 29 residues processed: 216 average time/residue: 0.2066 time to fit residues: 61.2526 Evaluate side-chains 207 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9339 Z= 0.200 Angle : 0.559 9.225 12662 Z= 0.280 Chirality : 0.040 0.155 1450 Planarity : 0.003 0.044 1555 Dihedral : 5.025 56.148 1596 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.00 % Allowed : 17.21 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1123 helix: 1.18 (0.26), residues: 426 sheet: -0.58 (0.29), residues: 288 loop : -1.08 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 102 PHE 0.011 0.001 PHE E 32 TYR 0.016 0.001 TYR A 296 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 39 LEU cc_start: 0.9179 (tp) cc_final: 0.8771 (tt) REVERT: R 81 LEU cc_start: 0.8575 (mt) cc_final: 0.8332 (mt) REVERT: R 90 LYS cc_start: 0.8166 (mttt) cc_final: 0.7851 (mmmm) REVERT: R 91 TRP cc_start: 0.8216 (t-100) cc_final: 0.7860 (t-100) REVERT: R 158 LEU cc_start: 0.7685 (mt) cc_final: 0.7449 (mt) REVERT: R 161 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8151 (t80) REVERT: R 191 LEU cc_start: 0.6905 (tp) cc_final: 0.6651 (pp) REVERT: R 269 LYS cc_start: 0.7965 (mptt) cc_final: 0.7650 (mtpt) REVERT: R 270 GLU cc_start: 0.7767 (mp0) cc_final: 0.7200 (tp30) REVERT: R 274 TYR cc_start: 0.7890 (m-80) cc_final: 0.7474 (m-10) REVERT: R 300 MET cc_start: 0.8864 (mtt) cc_final: 0.8515 (mtm) REVERT: A 48 THR cc_start: 0.8107 (m) cc_final: 0.7847 (p) REVERT: A 52 GLN cc_start: 0.7072 (tt0) cc_final: 0.6639 (tt0) REVERT: A 326 SER cc_start: 0.8122 (m) cc_final: 0.7561 (t) REVERT: B 10 GLU cc_start: 0.8157 (tp30) cc_final: 0.7793 (tp30) REVERT: B 234 PHE cc_start: 0.9336 (OUTLIER) cc_final: 0.8948 (m-80) REVERT: B 243 THR cc_start: 0.8642 (m) cc_final: 0.8303 (p) REVERT: B 267 ASP cc_start: 0.8835 (m-30) cc_final: 0.8427 (t0) REVERT: B 291 ASP cc_start: 0.8136 (t70) cc_final: 0.7790 (t70) REVERT: C 13 ARG cc_start: 0.8111 (ptp-110) cc_final: 0.7733 (ttm-80) REVERT: E 89 GLU cc_start: 0.7572 (tp30) cc_final: 0.7270 (tp30) REVERT: E 140 MET cc_start: 0.9059 (mmm) cc_final: 0.8348 (mmm) outliers start: 39 outliers final: 34 residues processed: 219 average time/residue: 0.2162 time to fit residues: 64.6436 Evaluate side-chains 214 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN E 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9339 Z= 0.219 Angle : 0.575 8.916 12662 Z= 0.289 Chirality : 0.040 0.156 1450 Planarity : 0.003 0.044 1555 Dihedral : 4.956 56.343 1596 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.20 % Allowed : 18.24 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1123 helix: 1.17 (0.26), residues: 425 sheet: -0.51 (0.29), residues: 288 loop : -1.09 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 95 HIS 0.004 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.017 0.001 TYR A 296 ARG 0.007 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 182 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 39 LEU cc_start: 0.9200 (tp) cc_final: 0.8773 (tt) REVERT: R 81 LEU cc_start: 0.8562 (mt) cc_final: 0.8313 (mt) REVERT: R 90 LYS cc_start: 0.8063 (mttt) cc_final: 0.7377 (ttmm) REVERT: R 91 TRP cc_start: 0.8212 (t-100) cc_final: 0.7915 (t-100) REVERT: R 158 LEU cc_start: 0.7643 (mt) cc_final: 0.7442 (mt) REVERT: R 161 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8169 (t80) REVERT: R 191 LEU cc_start: 0.6847 (tp) cc_final: 0.6626 (pp) REVERT: R 269 LYS cc_start: 0.7958 (mptt) cc_final: 0.7640 (mtpt) REVERT: R 270 GLU cc_start: 0.7647 (mp0) cc_final: 0.7151 (tp30) REVERT: R 274 TYR cc_start: 0.7893 (m-80) cc_final: 0.7501 (m-10) REVERT: R 293 PHE cc_start: 0.8598 (t80) cc_final: 0.8273 (t80) REVERT: R 300 MET cc_start: 0.8864 (mtt) cc_final: 0.8519 (mtm) REVERT: A 48 THR cc_start: 0.7927 (m) cc_final: 0.7717 (p) REVERT: A 242 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7466 (mtt90) REVERT: B 10 GLU cc_start: 0.8187 (tp30) cc_final: 0.7806 (tp30) REVERT: B 234 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8962 (m-80) REVERT: B 243 THR cc_start: 0.8654 (m) cc_final: 0.8334 (p) REVERT: B 267 ASP cc_start: 0.8753 (m-30) cc_final: 0.8355 (t0) REVERT: B 291 ASP cc_start: 0.8135 (t70) cc_final: 0.7778 (t70) REVERT: C 13 ARG cc_start: 0.8186 (ptp-110) cc_final: 0.7826 (ttm-80) REVERT: E 89 GLU cc_start: 0.7570 (tp30) cc_final: 0.7294 (tp30) REVERT: E 220 GLU cc_start: 0.8027 (mp0) cc_final: 0.7798 (mp0) outliers start: 41 outliers final: 37 residues processed: 212 average time/residue: 0.2187 time to fit residues: 63.5069 Evaluate side-chains 219 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 179 ASN A 304 GLN B 88 ASN E 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9339 Z= 0.197 Angle : 0.569 9.413 12662 Z= 0.285 Chirality : 0.040 0.154 1450 Planarity : 0.003 0.044 1555 Dihedral : 4.847 56.285 1596 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.89 % Allowed : 18.44 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1123 helix: 1.17 (0.26), residues: 425 sheet: -0.49 (0.29), residues: 290 loop : -1.10 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.017 0.001 TYR A 296 ARG 0.007 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7228 (ttp-110) cc_final: 0.6586 (mtm180) REVERT: R 39 LEU cc_start: 0.9190 (tp) cc_final: 0.8772 (tt) REVERT: R 81 LEU cc_start: 0.8570 (mt) cc_final: 0.8335 (mt) REVERT: R 90 LYS cc_start: 0.8010 (mttt) cc_final: 0.7332 (ttmm) REVERT: R 91 TRP cc_start: 0.8231 (t-100) cc_final: 0.7963 (t-100) REVERT: R 157 THR cc_start: 0.8250 (m) cc_final: 0.8035 (t) REVERT: R 158 LEU cc_start: 0.7698 (mt) cc_final: 0.7464 (mt) REVERT: R 161 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8149 (t80) REVERT: R 179 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.6410 (m110) REVERT: R 191 LEU cc_start: 0.6884 (tp) cc_final: 0.6653 (pp) REVERT: R 269 LYS cc_start: 0.7891 (mptt) cc_final: 0.7573 (mtpt) REVERT: R 270 GLU cc_start: 0.7628 (mp0) cc_final: 0.7151 (tp30) REVERT: R 274 TYR cc_start: 0.7890 (m-80) cc_final: 0.7375 (m-10) REVERT: R 293 PHE cc_start: 0.8578 (t80) cc_final: 0.8246 (t80) REVERT: R 300 MET cc_start: 0.8854 (mtt) cc_final: 0.8509 (mtm) REVERT: A 48 THR cc_start: 0.7919 (m) cc_final: 0.7704 (p) REVERT: A 242 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7495 (mtt90) REVERT: B 10 GLU cc_start: 0.8181 (tp30) cc_final: 0.7793 (tp30) REVERT: B 234 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8958 (m-80) REVERT: B 243 THR cc_start: 0.8616 (m) cc_final: 0.8297 (p) REVERT: B 267 ASP cc_start: 0.8735 (m-30) cc_final: 0.8325 (t0) REVERT: B 291 ASP cc_start: 0.8113 (t70) cc_final: 0.7748 (t70) REVERT: C 13 ARG cc_start: 0.8207 (ptp-110) cc_final: 0.7819 (ttm-80) REVERT: E 220 GLU cc_start: 0.8014 (mp0) cc_final: 0.7801 (mp0) outliers start: 38 outliers final: 31 residues processed: 219 average time/residue: 0.2253 time to fit residues: 66.4521 Evaluate side-chains 220 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9339 Z= 0.224 Angle : 0.587 9.291 12662 Z= 0.293 Chirality : 0.041 0.156 1450 Planarity : 0.003 0.041 1555 Dihedral : 4.875 56.860 1596 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.59 % Allowed : 18.65 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1123 helix: 1.18 (0.26), residues: 424 sheet: -0.45 (0.28), residues: 298 loop : -1.12 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 95 HIS 0.004 0.001 HIS R 102 PHE 0.009 0.001 PHE A 189 TYR 0.017 0.001 TYR A 296 ARG 0.007 0.000 ARG A 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.053 Fit side-chains REVERT: R 26 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6592 (mtm180) REVERT: R 39 LEU cc_start: 0.9203 (tp) cc_final: 0.8768 (tt) REVERT: R 81 LEU cc_start: 0.8584 (mt) cc_final: 0.8356 (mt) REVERT: R 90 LYS cc_start: 0.7993 (mttt) cc_final: 0.7315 (ttmm) REVERT: R 91 TRP cc_start: 0.8239 (t-100) cc_final: 0.7994 (t-100) REVERT: R 157 THR cc_start: 0.8289 (m) cc_final: 0.8066 (t) REVERT: R 158 LEU cc_start: 0.7713 (mt) cc_final: 0.7488 (mt) REVERT: R 161 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8160 (t80) REVERT: R 179 ASN cc_start: 0.7731 (t0) cc_final: 0.6276 (m110) REVERT: R 191 LEU cc_start: 0.6908 (tp) cc_final: 0.6671 (pp) REVERT: R 269 LYS cc_start: 0.7869 (mptt) cc_final: 0.7543 (mtpt) REVERT: R 270 GLU cc_start: 0.7671 (mp0) cc_final: 0.7124 (tp30) REVERT: R 274 TYR cc_start: 0.7892 (m-80) cc_final: 0.7362 (m-10) REVERT: R 293 PHE cc_start: 0.8596 (t80) cc_final: 0.8266 (t80) REVERT: R 300 MET cc_start: 0.8859 (mtt) cc_final: 0.8517 (mtm) REVERT: A 242 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7500 (mtt90) REVERT: B 234 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8957 (m-80) REVERT: B 243 THR cc_start: 0.8659 (m) cc_final: 0.8351 (p) REVERT: B 267 ASP cc_start: 0.8747 (m-30) cc_final: 0.8336 (t0) REVERT: B 291 ASP cc_start: 0.8126 (t70) cc_final: 0.7758 (t70) REVERT: C 13 ARG cc_start: 0.8223 (ptp-110) cc_final: 0.7846 (ttm-80) REVERT: E 89 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7422 (tp30) REVERT: E 140 MET cc_start: 0.9078 (mmm) cc_final: 0.8554 (mmm) REVERT: E 220 GLU cc_start: 0.7980 (mp0) cc_final: 0.7751 (mp0) outliers start: 35 outliers final: 32 residues processed: 211 average time/residue: 0.2135 time to fit residues: 61.7192 Evaluate side-chains 217 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 77 optimal weight: 0.0060 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104437 restraints weight = 13457.408| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.33 r_work: 0.3165 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9339 Z= 0.190 Angle : 0.571 9.521 12662 Z= 0.285 Chirality : 0.040 0.153 1450 Planarity : 0.003 0.041 1555 Dihedral : 4.769 56.361 1596 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.59 % Allowed : 18.55 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1123 helix: 1.28 (0.26), residues: 422 sheet: -0.36 (0.29), residues: 291 loop : -1.09 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.018 0.001 TYR A 296 ARG 0.007 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2527.30 seconds wall clock time: 46 minutes 5.66 seconds (2765.66 seconds total)