Starting phenix.real_space_refine on Tue Sep 24 08:07:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6i_31481/09_2024/7f6i_31481.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6i_31481/09_2024/7f6i_31481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6i_31481/09_2024/7f6i_31481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6i_31481/09_2024/7f6i_31481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6i_31481/09_2024/7f6i_31481.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6i_31481/09_2024/7f6i_31481.cif" } resolution = 2.8 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= 0.004 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 57 5.16 5 C 4724 2.51 5 N 1244 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7361 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2448 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 3, 'TRANS': 6} Chain: "B" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1867 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 1 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2507 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 321} Chain: "D" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 371 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.54, per 1000 atoms: 0.62 Number of scatterers: 7361 At special positions: 0 Unit cell: (104.442, 94.302, 120.666, 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 57 16.00 O 1336 8.00 N 1244 7.00 C 4724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 211 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 45.1% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 50 through 85 removed outlier: 3.756A pdb=" N GLY A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 3.655A pdb=" N HIS A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 108 removed outlier: 3.663A pdb=" N TYR A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 119 removed outlier: 3.946A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 160 removed outlier: 4.091A pdb=" N LEU A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.740A pdb=" N ARG A 169 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 189 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.594A pdb=" N LEU A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.892A pdb=" N GLU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.804A pdb=" N MET A 256 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 257 " --> pdb=" O ASN A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 257' Processing helix chain 'A' and resid 264 through 298 removed outlier: 3.973A pdb=" N ALA A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 303 through 321 removed outlier: 4.061A pdb=" N PHE A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.815A pdb=" N CYS A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'B' and resid 15 through 36 Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 212 through 217 removed outlier: 4.061A pdb=" N TRP B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 246 through 261 removed outlier: 3.615A pdb=" N TYR B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 removed outlier: 3.566A pdb=" N GLN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.695A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.542A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 201 Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 196 removed outlier: 6.444A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N SER B 225 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LYS B 41 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N MET B 227 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B 43 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 229 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 45 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ALA B 231 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 226 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE B 272 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE B 228 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 274 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 230 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.761A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.656A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.852A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.646A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.621A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.931A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1041 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: 1.95 Time building geometry restraints manager: 2.13 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: 2361 1.34 - 1.46: 1415 1.46 - 1.58: 3658 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 7518 Sorted by residual: bond pdb=" C10 CLR A 503 " pdb=" C5 CLR A 503 " ideal model delta sigma weight residual 1.519 1.401 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C10 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C4 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.506 1.392 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C10 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C4 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.506 1.395 0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 7513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 9606 1.82 - 3.64: 511 3.64 - 5.47: 63 5.47 - 7.29: 21 7.29 - 9.11: 4 Bond angle restraints: 10205 Sorted by residual: angle pdb=" N PHE A 259 " pdb=" CA PHE A 259 " pdb=" C PHE A 259 " ideal model delta sigma weight residual 113.20 106.01 7.19 1.21e+00 6.83e-01 3.53e+01 angle pdb=" CA GLN B 197 " pdb=" C GLN B 197 " pdb=" O GLN B 197 " ideal model delta sigma weight residual 122.27 117.41 4.86 1.16e+00 7.43e-01 1.75e+01 angle pdb=" N ASN A 254 " pdb=" CA ASN A 254 " pdb=" C ASN A 254 " ideal model delta sigma weight residual 113.02 108.55 4.47 1.20e+00 6.94e-01 1.39e+01 angle pdb=" N GLU A 255 " pdb=" CA GLU A 255 " pdb=" C GLU A 255 " ideal model delta sigma weight residual 113.19 108.77 4.42 1.19e+00 7.06e-01 1.38e+01 angle pdb=" N VAL C 90 " pdb=" CA VAL C 90 " pdb=" C VAL C 90 " ideal model delta sigma weight residual 111.67 108.14 3.53 9.50e-01 1.11e+00 1.38e+01 ... (remaining 10200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 4426 24.42 - 48.83: 175 48.83 - 73.25: 26 73.25 - 97.67: 4 97.67 - 122.08: 3 Dihedral angle restraints: 4634 sinusoidal: 1965 harmonic: 2669 Sorted by residual: dihedral pdb=" CB CYS A 130 " pdb=" SG CYS A 130 " pdb=" SG CYS A 211 " pdb=" CB CYS A 211 " ideal model delta sinusoidal sigma weight residual -86.00 -170.09 84.09 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS A 47 " pdb=" SG CYS A 47 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 151.56 -58.56 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N TYR B 291 " pdb=" CA TYR B 291 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 4631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1053 0.094 - 0.189: 105 0.189 - 0.283: 8 0.283 - 0.377: 4 0.377 - 0.472: 6 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C14 CLR A 503 " pdb=" C13 CLR A 503 " pdb=" C15 CLR A 503 " pdb=" C8 CLR A 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" C14 CLR A 502 " pdb=" C13 CLR A 502 " pdb=" C15 CLR A 502 " pdb=" C8 CLR A 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" C14 CLR A 501 " pdb=" C13 CLR A 501 " pdb=" C15 CLR A 501 " pdb=" C8 CLR A 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 1173 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 38 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO C 39 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 55 " -0.023 2.00e-02 2.50e+03 1.67e-02 4.90e+00 pdb=" CG PHE B 55 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 55 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 55 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 55 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 55 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 55 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 42 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ARG C 42 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG C 42 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE C 43 " 0.012 2.00e-02 2.50e+03 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1209 2.76 - 3.30: 6925 3.30 - 3.83: 12054 3.83 - 4.37: 14786 4.37 - 4.90: 25270 Nonbonded interactions: 60244 Sorted by model distance: nonbonded pdb=" OG1 THR A 314 " pdb=" NH2 ARG L 10 " model vdw 2.227 3.120 nonbonded pdb=" NE ARG C 251 " pdb=" OE2 GLU C 260 " model vdw 2.257 3.120 nonbonded pdb=" OG SER A 318 " pdb=" OG SER L 7 " model vdw 2.331 3.040 nonbonded pdb=" OG SER C 108 " pdb=" OD1 ASP C 154 " model vdw 2.368 3.040 nonbonded pdb=" OG SER C 147 " pdb=" O VAL C 187 " model vdw 2.400 3.040 ... (remaining 60239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.080 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.870 Find NCS groups from input model: 0.070 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.008 0.118 7518 Z= 0.504 Angle : 0.922 9.110 10205 Z= 0.554 Chirality : 0.067 0.472 1176 Planarity : 0.005 0.066 1270 Dihedral : 13.558 122.083 2894 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.50 % Allowed : 0.99 % Favored : 98.51 % Cbeta Deviations : 0.12 % 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: 0.20 (0.27), residues: 903 helix: 1.40 (0.26), residues: 387 sheet: -0.03 (0.39), residues: 184 loop : -1.26 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 283 HIS 0.008 0.001 HIS C 54 PHE 0.035 0.002 PHE B 55 TYR 0.014 0.002 TYR A 347 ARG 0.020 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 0.813 Fit side-chains REVERT: C 340 ASN cc_start: 0.8017 (t0) cc_final: 0.7806 (t0) outliers start: 4 outliers final: 1 residues processed: 123 average time/residue: 1.3177 time to fit residues: 170.1959 Evaluate side-chains 86 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 254 ASN A 324 ASN B 265 GLN C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7518 Z= 0.223 Angle : 0.585 7.291 10205 Z= 0.305 Chirality : 0.044 0.207 1176 Planarity : 0.004 0.055 1270 Dihedral : 8.750 90.800 1190 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.74 % Allowed : 10.19 % Favored : 88.07 % 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: 0.66 (0.27), residues: 903 helix: 2.03 (0.26), residues: 383 sheet: 0.16 (0.38), residues: 179 loop : -1.29 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.025 0.002 PHE B 55 TYR 0.010 0.001 TYR B 291 ARG 0.008 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.774 Fit side-chains REVERT: B 19 ARG cc_start: 0.7284 (mmm-85) cc_final: 0.6788 (mmm160) REVERT: D 21 MET cc_start: 0.6126 (tmm) cc_final: 0.5814 (tmm) outliers start: 14 outliers final: 5 residues processed: 113 average time/residue: 1.1514 time to fit residues: 138.2640 Evaluate side-chains 103 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 249 GLN A 315 GLN A 324 ASN C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7518 Z= 0.194 Angle : 0.553 8.674 10205 Z= 0.286 Chirality : 0.043 0.194 1176 Planarity : 0.004 0.049 1270 Dihedral : 7.304 61.391 1190 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.61 % Allowed : 12.05 % Favored : 85.34 % 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: 0.92 (0.27), residues: 903 helix: 2.35 (0.26), residues: 382 sheet: 0.25 (0.37), residues: 184 loop : -1.28 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS B 287 PHE 0.026 0.001 PHE B 55 TYR 0.016 0.001 TYR A 177 ARG 0.008 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 0.897 Fit side-chains REVERT: A 262 ILE cc_start: 0.8020 (mp) cc_final: 0.7757 (pp) REVERT: C 217 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7165 (ppp) outliers start: 21 outliers final: 9 residues processed: 112 average time/residue: 1.1303 time to fit residues: 134.2265 Evaluate side-chains 100 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7518 Z= 0.187 Angle : 0.528 6.411 10205 Z= 0.277 Chirality : 0.042 0.197 1176 Planarity : 0.004 0.044 1270 Dihedral : 6.259 59.232 1190 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.98 % Allowed : 12.67 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.28), residues: 903 helix: 2.51 (0.26), residues: 382 sheet: 0.14 (0.36), residues: 187 loop : -1.24 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS B 287 PHE 0.020 0.001 PHE B 55 TYR 0.019 0.001 TYR A 177 ARG 0.009 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.844 Fit side-chains REVERT: A 262 ILE cc_start: 0.7924 (mp) cc_final: 0.7718 (pp) REVERT: C 152 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8310 (tt) outliers start: 24 outliers final: 11 residues processed: 104 average time/residue: 1.0773 time to fit residues: 119.5170 Evaluate side-chains 106 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 7518 Z= 0.441 Angle : 0.693 10.387 10205 Z= 0.359 Chirality : 0.049 0.179 1176 Planarity : 0.005 0.058 1270 Dihedral : 6.976 59.676 1190 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.11 % Allowed : 13.79 % 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: 0.47 (0.27), residues: 903 helix: 1.86 (0.27), residues: 381 sheet: -0.11 (0.38), residues: 176 loop : -1.23 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.006 0.001 HIS C 311 PHE 0.028 0.003 PHE B 55 TYR 0.021 0.002 TYR A 177 ARG 0.008 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.909 Fit side-chains REVERT: A 200 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: A 322 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: C 219 ARG cc_start: 0.7570 (mmt90) cc_final: 0.7322 (mmt90) REVERT: D 21 MET cc_start: 0.6501 (tmm) cc_final: 0.6170 (tmm) outliers start: 25 outliers final: 11 residues processed: 106 average time/residue: 1.1943 time to fit residues: 134.3542 Evaluate side-chains 101 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN A 287 GLN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7518 Z= 0.182 Angle : 0.533 6.446 10205 Z= 0.281 Chirality : 0.042 0.192 1176 Planarity : 0.004 0.042 1270 Dihedral : 6.441 59.377 1190 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.86 % Allowed : 14.53 % Favored : 82.61 % 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: 0.82 (0.28), residues: 903 helix: 2.37 (0.27), residues: 382 sheet: -0.22 (0.36), residues: 189 loop : -1.21 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.002 0.001 HIS B 287 PHE 0.024 0.001 PHE B 55 TYR 0.022 0.001 TYR A 177 ARG 0.010 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.749 Fit side-chains REVERT: A 200 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: B 197 GLN cc_start: 0.6262 (mt0) cc_final: 0.6022 (tt0) REVERT: B 356 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: C 152 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8338 (tt) REVERT: C 219 ARG cc_start: 0.7511 (mmt90) cc_final: 0.7288 (mmt90) REVERT: D 21 MET cc_start: 0.6535 (tmm) cc_final: 0.6230 (tmm) outliers start: 23 outliers final: 10 residues processed: 108 average time/residue: 1.1863 time to fit residues: 135.6262 Evaluate side-chains 105 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7518 Z= 0.250 Angle : 0.580 7.363 10205 Z= 0.303 Chirality : 0.044 0.185 1176 Planarity : 0.004 0.049 1270 Dihedral : 6.490 59.324 1190 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.35 % Allowed : 14.41 % Favored : 82.24 % 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: 0.77 (0.28), residues: 903 helix: 2.30 (0.27), residues: 382 sheet: -0.19 (0.37), residues: 179 loop : -1.19 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 123 HIS 0.003 0.001 HIS C 311 PHE 0.028 0.002 PHE B 55 TYR 0.024 0.002 TYR A 177 ARG 0.013 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.746 Fit side-chains REVERT: A 200 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: B 197 GLN cc_start: 0.6372 (mt0) cc_final: 0.6061 (tt0) REVERT: B 356 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: D 21 MET cc_start: 0.6350 (tmm) cc_final: 0.5865 (tmm) outliers start: 27 outliers final: 15 residues processed: 108 average time/residue: 1.1271 time to fit residues: 129.1053 Evaluate side-chains 108 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7518 Z= 0.165 Angle : 0.518 5.747 10205 Z= 0.273 Chirality : 0.042 0.193 1176 Planarity : 0.004 0.051 1270 Dihedral : 6.262 59.838 1190 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.73 % Allowed : 15.03 % Favored : 82.24 % 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: 0.95 (0.28), residues: 903 helix: 2.58 (0.27), residues: 382 sheet: -0.34 (0.36), residues: 186 loop : -1.14 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 PHE 0.032 0.001 PHE B 55 TYR 0.026 0.001 TYR A 177 ARG 0.012 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 200 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: A 322 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: B 197 GLN cc_start: 0.6308 (mt0) cc_final: 0.6021 (tt0) REVERT: C 217 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7117 (ppp) REVERT: D 21 MET cc_start: 0.6454 (tmm) cc_final: 0.6163 (tmm) outliers start: 22 outliers final: 13 residues processed: 110 average time/residue: 1.1216 time to fit residues: 131.1152 Evaluate side-chains 108 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN A 315 GLN C 237 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7518 Z= 0.200 Angle : 0.553 6.305 10205 Z= 0.291 Chirality : 0.043 0.189 1176 Planarity : 0.004 0.052 1270 Dihedral : 6.299 59.939 1190 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.86 % Allowed : 15.53 % Favored : 81.61 % 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: 0.93 (0.28), residues: 903 helix: 2.57 (0.27), residues: 382 sheet: -0.33 (0.36), residues: 184 loop : -1.15 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 PHE 0.031 0.002 PHE B 55 TYR 0.028 0.002 TYR A 177 ARG 0.013 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.841 Fit side-chains REVERT: A 200 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: A 322 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: B 197 GLN cc_start: 0.6292 (mt0) cc_final: 0.6003 (tt0) REVERT: B 356 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: C 217 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7182 (ppp) outliers start: 23 outliers final: 11 residues processed: 107 average time/residue: 1.0937 time to fit residues: 124.3813 Evaluate side-chains 106 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.0270 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7518 Z= 0.201 Angle : 0.558 6.756 10205 Z= 0.293 Chirality : 0.043 0.189 1176 Planarity : 0.005 0.056 1270 Dihedral : 6.296 59.270 1190 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.36 % Allowed : 16.27 % Favored : 81.37 % 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: 0.93 (0.28), residues: 903 helix: 2.55 (0.27), residues: 382 sheet: -0.35 (0.36), residues: 184 loop : -1.13 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 PHE 0.036 0.001 PHE B 55 TYR 0.029 0.002 TYR A 177 ARG 0.014 0.001 ARG B 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.891 Fit side-chains REVERT: A 322 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: B 356 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: C 217 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7190 (ppp) outliers start: 19 outliers final: 11 residues processed: 104 average time/residue: 1.1000 time to fit residues: 121.7043 Evaluate side-chains 106 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN A 315 GLN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122867 restraints weight = 8128.667| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.87 r_work: 0.3161 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7518 Z= 0.201 Angle : 0.564 6.807 10205 Z= 0.296 Chirality : 0.043 0.189 1176 Planarity : 0.005 0.057 1270 Dihedral : 6.280 59.375 1190 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.36 % Allowed : 16.65 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.28), residues: 903 helix: 2.53 (0.27), residues: 383 sheet: -0.35 (0.36), residues: 183 loop : -1.14 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 PHE 0.034 0.001 PHE B 55 TYR 0.030 0.002 TYR A 177 ARG 0.014 0.001 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.17 seconds wall clock time: 51 minutes 34.97 seconds (3094.97 seconds total)