Starting phenix.real_space_refine on Mon Mar 11 11:18:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/03_2024/8hmv_34903.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/03_2024/8hmv_34903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/03_2024/8hmv_34903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/03_2024/8hmv_34903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/03_2024/8hmv_34903.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/03_2024/8hmv_34903.pdb" } resolution = 2.91 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= 0.035 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 52 5.16 5 C 5168 2.51 5 N 1410 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8127 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2237 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Chain: "C" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1892 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" 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: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 4.95, per 1000 atoms: 0.61 Number of scatterers: 8127 At special positions: 0 Unit cell: (79.9, 103.7, 128.35, 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 52 16.00 O 1497 8.00 N 1410 7.00 C 5168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 3.02 Conformation dependent library (CDL) restraints added in 1.7 seconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.9% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 30 through 55 Processing helix chain 'A' and resid 63 through 82 removed outlier: 4.155A pdb=" N PHE A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 97 through 133 removed outlier: 3.579A pdb=" N PHE A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 142 through 161 removed outlier: 3.952A pdb=" N PHE A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.627A pdb=" N ASP A 176 " --> pdb=" O TYR A 173 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 177 " --> pdb=" O HIS A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 188 through 233 removed outlier: 5.055A pdb=" N ALA A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Proline residue: A 202 - end of helix removed outlier: 3.866A pdb=" N VAL A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 278 removed outlier: 3.535A pdb=" N ARG A 256 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 282 through 306 removed outlier: 4.038A pdb=" N PHE A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.956A pdb=" N ALA C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.569A pdb=" N ILE C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 removed outlier: 3.617A pdb=" N GLN C 236 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS C 237 " --> pdb=" O TRP C 234 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 238 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 239 " --> pdb=" O GLN C 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 239' Processing helix chain 'C' and resid 264 through 279 removed outlier: 3.934A pdb=" N GLU C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 removed outlier: 4.188A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.540A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 331 through 350 removed outlier: 3.735A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.838A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.696A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.863A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 210 through 214 removed outlier: 6.362A pdb=" N HIS C 41 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N PHE C 222 " --> pdb=" O HIS C 41 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 43 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N ALA C 243 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG C 42 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ILE C 245 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 44 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL C 247 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 46 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.632A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.028A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.253A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.680A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.643A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.625A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.606A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.591A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.889A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1104 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: 2.35 Time building geometry restraints manager: 3.29 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: 2638 1.34 - 1.46: 1404 1.46 - 1.57: 4192 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 8305 Sorted by residual: bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.64e+00 bond pdb=" CG1 ILE B 123 " pdb=" CD1 ILE B 123 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.23e+00 bond pdb=" C HIS A 61 " pdb=" O HIS A 61 " ideal model delta sigma weight residual 1.235 1.246 -0.011 1.10e-02 8.26e+03 1.07e+00 bond pdb=" CB ASN C 239 " pdb=" CG ASN C 239 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 9.50e-01 bond pdb=" CB THR B 274 " pdb=" CG2 THR B 274 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.48e-01 ... (remaining 8300 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.89: 122 105.89 - 112.94: 4442 112.94 - 119.99: 2864 119.99 - 127.04: 3729 127.04 - 134.09: 99 Bond angle restraints: 11256 Sorted by residual: angle pdb=" N ASN A 60 " pdb=" CA ASN A 60 " pdb=" C ASN A 60 " ideal model delta sigma weight residual 111.71 107.92 3.79 1.34e+00 5.57e-01 8.01e+00 angle pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" C PHE B 234 " ideal model delta sigma weight residual 110.50 114.31 -3.81 1.41e+00 5.03e-01 7.32e+00 angle pdb=" C SER B 74 " pdb=" N GLN B 75 " pdb=" CA GLN B 75 " ideal model delta sigma weight residual 120.31 124.27 -3.96 1.52e+00 4.33e-01 6.79e+00 angle pdb=" C GLY A 169 " pdb=" N LYS A 170 " pdb=" CA LYS A 170 " ideal model delta sigma weight residual 121.59 130.41 -8.82 3.54e+00 7.98e-02 6.21e+00 angle pdb=" CA GLN A 103 " pdb=" CB GLN A 103 " pdb=" CG GLN A 103 " ideal model delta sigma weight residual 114.10 118.76 -4.66 2.00e+00 2.50e-01 5.43e+00 ... (remaining 11251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 4470 17.26 - 34.51: 373 34.51 - 51.77: 59 51.77 - 69.02: 12 69.02 - 86.28: 8 Dihedral angle restraints: 4922 sinusoidal: 1940 harmonic: 2982 Sorted by residual: dihedral pdb=" CA PRO A 57 " pdb=" C PRO A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 -143.08 -36.92 0 5.00e+00 4.00e-02 5.45e+01 dihedral pdb=" CA LEU C 291 " pdb=" C LEU C 291 " pdb=" N ASN C 292 " pdb=" CA ASN C 292 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 4919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 639 0.028 - 0.056: 372 0.056 - 0.084: 162 0.084 - 0.112: 68 0.112 - 0.140: 24 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA ILE B 43 " pdb=" N ILE B 43 " pdb=" C ILE B 43 " pdb=" CB ILE B 43 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA TRP A 291 " pdb=" N TRP A 291 " pdb=" C TRP A 291 " pdb=" CB TRP A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1262 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 56 " -0.045 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO A 57 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 266 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO A 267 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 162 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.30e+00 pdb=" N PRO A 163 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.021 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 203 2.70 - 3.25: 7636 3.25 - 3.80: 12121 3.80 - 4.35: 16263 4.35 - 4.90: 28420 Nonbonded interactions: 64643 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.150 2.440 nonbonded pdb=" OH TYR C 318 " pdb=" OD2 ASP C 343 " model vdw 2.155 2.440 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.213 2.440 nonbonded pdb=" OD1 ASN C 239 " pdb=" NZ LYS B 57 " model vdw 2.232 2.520 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.240 2.520 ... (remaining 64638 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.220 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.030 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 0.050 8305 Z= 0.337 Angle : 0.635 8.822 11256 Z= 0.361 Chirality : 0.045 0.140 1265 Planarity : 0.004 0.069 1431 Dihedral : 13.376 86.277 2984 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.72 (0.26), residues: 1004 helix: 0.72 (0.26), residues: 400 sheet: -1.04 (0.32), residues: 229 loop : -1.30 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 291 HIS 0.010 0.001 HIS C 357 PHE 0.018 0.002 PHE A 272 TYR 0.016 0.002 TYR C 358 ARG 0.005 0.000 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.006 Fit side-chains REVERT: C 274 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7930 (ttmt) REVERT: B 36 ASN cc_start: 0.7654 (m-40) cc_final: 0.7354 (m-40) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 1.7340 time to fit residues: 177.6627 Evaluate side-chains 83 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 57 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8305 Z= 0.160 Angle : 0.488 7.123 11256 Z= 0.263 Chirality : 0.041 0.127 1265 Planarity : 0.004 0.064 1431 Dihedral : 4.439 35.955 1116 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.01 % Allowed : 6.64 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.02 (0.26), residues: 1004 helix: 1.45 (0.27), residues: 400 sheet: -0.40 (0.33), residues: 213 loop : -1.32 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 291 HIS 0.007 0.001 HIS C 220 PHE 0.012 0.001 PHE B 151 TYR 0.011 0.001 TYR C 358 ARG 0.001 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.966 Fit side-chains REVERT: C 274 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7896 (ttmt) REVERT: B 25 CYS cc_start: 0.7702 (t) cc_final: 0.7461 (t) REVERT: B 36 ASN cc_start: 0.7675 (m-40) cc_final: 0.7411 (m-40) REVERT: B 217 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7394 (ptt) outliers start: 9 outliers final: 3 residues processed: 98 average time/residue: 1.6267 time to fit residues: 167.3679 Evaluate side-chains 93 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8305 Z= 0.232 Angle : 0.516 7.205 11256 Z= 0.275 Chirality : 0.042 0.135 1265 Planarity : 0.004 0.061 1431 Dihedral : 4.395 34.342 1116 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.24 % Allowed : 10.36 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.10 (0.26), residues: 1004 helix: 1.61 (0.27), residues: 400 sheet: -0.34 (0.33), residues: 218 loop : -1.32 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 291 HIS 0.008 0.001 HIS C 357 PHE 0.014 0.002 PHE A 298 TYR 0.014 0.001 TYR C 358 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.944 Fit side-chains REVERT: C 60 MET cc_start: 0.5760 (mpt) cc_final: 0.5474 (mpt) REVERT: C 274 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7905 (ttmt) REVERT: C 294 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: B 25 CYS cc_start: 0.7770 (t) cc_final: 0.7424 (t) REVERT: B 36 ASN cc_start: 0.7696 (m-40) cc_final: 0.7465 (m-40) REVERT: B 52 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7482 (mtp-110) REVERT: B 217 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7425 (ptt) outliers start: 11 outliers final: 3 residues processed: 97 average time/residue: 1.5638 time to fit residues: 159.2338 Evaluate side-chains 93 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8305 Z= 0.211 Angle : 0.494 7.075 11256 Z= 0.264 Chirality : 0.042 0.131 1265 Planarity : 0.004 0.060 1431 Dihedral : 4.288 33.541 1116 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.46 % Allowed : 11.82 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.32 (0.27), residues: 1004 helix: 1.76 (0.27), residues: 406 sheet: -0.22 (0.33), residues: 218 loop : -1.23 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 291 HIS 0.007 0.001 HIS C 357 PHE 0.014 0.002 PHE B 151 TYR 0.014 0.001 TYR B 105 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.934 Fit side-chains REVERT: C 268 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6982 (tp30) REVERT: C 274 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7875 (ttmt) REVERT: B 36 ASN cc_start: 0.7732 (m-40) cc_final: 0.7503 (m-40) REVERT: B 52 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7452 (mtp-110) REVERT: B 217 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7416 (ptt) outliers start: 13 outliers final: 3 residues processed: 94 average time/residue: 1.4989 time to fit residues: 148.2068 Evaluate side-chains 95 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8305 Z= 0.297 Angle : 0.556 7.800 11256 Z= 0.296 Chirality : 0.044 0.139 1265 Planarity : 0.004 0.059 1431 Dihedral : 4.468 32.848 1116 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.03 % Allowed : 12.39 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.20 (0.27), residues: 1004 helix: 1.64 (0.26), residues: 406 sheet: -0.25 (0.33), residues: 218 loop : -1.29 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 291 HIS 0.009 0.001 HIS C 357 PHE 0.016 0.002 PHE B 151 TYR 0.020 0.002 TYR B 105 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.013 Fit side-chains REVERT: C 268 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7010 (tp30) REVERT: C 274 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7924 (ttmt) REVERT: B 36 ASN cc_start: 0.7736 (m-40) cc_final: 0.7488 (m-40) REVERT: B 52 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7489 (mtp-110) REVERT: B 217 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7394 (ptt) outliers start: 18 outliers final: 7 residues processed: 95 average time/residue: 1.5721 time to fit residues: 156.8748 Evaluate side-chains 97 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.003 0.032 8305 Z= 0.170 Angle : 0.471 6.863 11256 Z= 0.253 Chirality : 0.041 0.126 1265 Planarity : 0.004 0.058 1431 Dihedral : 4.166 32.002 1116 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.35 % Allowed : 13.74 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.49 (0.27), residues: 1004 helix: 1.87 (0.27), residues: 407 sheet: -0.01 (0.34), residues: 214 loop : -1.18 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 291 HIS 0.006 0.001 HIS C 357 PHE 0.014 0.001 PHE B 292 TYR 0.011 0.001 TYR C 339 ARG 0.003 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.948 Fit side-chains REVERT: C 268 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: C 274 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7877 (ttmt) REVERT: C 294 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6689 (mp10) REVERT: B 36 ASN cc_start: 0.7750 (m-40) cc_final: 0.7541 (m-40) outliers start: 12 outliers final: 6 residues processed: 100 average time/residue: 1.4928 time to fit residues: 156.9884 Evaluate side-chains 98 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN C 294 GLN B 75 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8305 Z= 0.162 Angle : 0.462 6.677 11256 Z= 0.248 Chirality : 0.041 0.140 1265 Planarity : 0.004 0.057 1431 Dihedral : 4.023 29.936 1116 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.35 % Allowed : 14.41 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 1004 helix: 2.05 (0.27), residues: 401 sheet: 0.08 (0.34), residues: 210 loop : -1.21 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 291 HIS 0.006 0.001 HIS C 357 PHE 0.022 0.001 PHE A 298 TYR 0.011 0.001 TYR C 37 ARG 0.002 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.877 Fit side-chains REVERT: C 60 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5498 (mpt) REVERT: C 268 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6982 (tp30) REVERT: C 294 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.6001 (mp-120) REVERT: B 52 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7661 (mtp180) outliers start: 12 outliers final: 6 residues processed: 97 average time/residue: 1.6510 time to fit residues: 168.0594 Evaluate side-chains 96 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8305 Z= 0.402 Angle : 0.606 8.327 11256 Z= 0.319 Chirality : 0.046 0.151 1265 Planarity : 0.005 0.057 1431 Dihedral : 4.500 30.363 1116 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.91 % Allowed : 14.53 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.23 (0.27), residues: 1004 helix: 1.66 (0.26), residues: 406 sheet: -0.20 (0.34), residues: 218 loop : -1.30 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 185 HIS 0.010 0.001 HIS C 357 PHE 0.020 0.002 PHE B 234 TYR 0.019 0.002 TYR C 339 ARG 0.005 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.019 Fit side-chains REVERT: C 268 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: B 52 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7650 (mtp180) outliers start: 17 outliers final: 10 residues processed: 97 average time/residue: 1.5161 time to fit residues: 154.7485 Evaluate side-chains 97 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 52 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.0000 chunk 91 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8305 Z= 0.208 Angle : 0.502 7.319 11256 Z= 0.268 Chirality : 0.042 0.138 1265 Planarity : 0.004 0.057 1431 Dihedral : 4.226 30.274 1116 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.35 % Allowed : 15.43 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.27), residues: 1004 helix: 1.86 (0.27), residues: 406 sheet: -0.11 (0.34), residues: 218 loop : -1.21 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 291 HIS 0.006 0.001 HIS C 357 PHE 0.018 0.002 PHE B 292 TYR 0.014 0.001 TYR C 339 ARG 0.002 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.989 Fit side-chains REVERT: C 60 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5481 (mpt) REVERT: C 268 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6980 (tp30) REVERT: B 52 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7642 (mtp180) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 1.5306 time to fit residues: 146.5916 Evaluate side-chains 95 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8305 Z= 0.202 Angle : 0.493 7.077 11256 Z= 0.263 Chirality : 0.041 0.129 1265 Planarity : 0.004 0.057 1431 Dihedral : 4.141 29.186 1116 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.13 % Allowed : 15.77 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 1004 helix: 1.92 (0.26), residues: 407 sheet: -0.07 (0.34), residues: 218 loop : -1.16 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 291 HIS 0.006 0.001 HIS C 357 PHE 0.017 0.001 PHE B 292 TYR 0.013 0.001 TYR C 339 ARG 0.002 0.000 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.977 Fit side-chains REVERT: C 60 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5503 (mpt) REVERT: C 268 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: B 52 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7661 (mtp180) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 1.5681 time to fit residues: 141.7751 Evaluate side-chains 91 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 294 GLN C 390 GLN B 88 ASN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110540 restraints weight = 9647.901| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.95 r_work: 0.3103 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8305 Z= 0.149 Angle : 0.450 6.439 11256 Z= 0.241 Chirality : 0.040 0.124 1265 Planarity : 0.004 0.056 1431 Dihedral : 3.908 28.152 1116 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.35 % Allowed : 15.65 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1004 helix: 2.15 (0.27), residues: 399 sheet: 0.16 (0.35), residues: 210 loop : -1.14 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 291 HIS 0.005 0.001 HIS C 357 PHE 0.016 0.001 PHE A 298 TYR 0.011 0.001 TYR A 211 ARG 0.008 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3424.89 seconds wall clock time: 61 minutes 25.66 seconds (3685.66 seconds total)