Starting phenix.real_space_refine on Fri Nov 15 08:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh6_39282/11_2024/8yh6_39282.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh6_39282/11_2024/8yh6_39282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh6_39282/11_2024/8yh6_39282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh6_39282/11_2024/8yh6_39282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh6_39282/11_2024/8yh6_39282.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh6_39282/11_2024/8yh6_39282.cif" } resolution = 3.62 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= 0.005 sd= 1.069 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: 6 Type Number sf(0) Gaussians I 1 10.91 5 S 66 5.16 5 Cl 1 4.86 5 C 5570 2.51 5 N 1464 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8706 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1705 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'XS0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.05, per 1000 atoms: 0.58 Number of scatterers: 8706 At special positions: 0 Unit cell: (91.02, 123.21, 127.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 1 52.95 Cl 1 17.00 S 66 16.00 O 1604 8.00 N 1464 7.00 C 5570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=1.70 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 37.3% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.637A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.833A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 22 Processing helix chain 'G' and resid 33 through 44 removed outlier: 3.556A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.529A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.928A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'R' and resid 10 through 40 Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 64 Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 79 through 115 Processing helix chain 'R' and resid 116 through 122 removed outlier: 4.435A pdb=" N ARG R 120 " --> pdb=" O VAL R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.574A pdb=" N VAL R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 removed outlier: 3.570A pdb=" N MET R 176 " --> pdb=" O ARG R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 Proline residue: R 244 - end of helix Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.824A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 295 Processing helix chain 'A' and resid 6 through 31 removed outlier: 4.118A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.886A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.615A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.994A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.673A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.301A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.007A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.517A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.912A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.515A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.191A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.636A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.143A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.270A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1170 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: 2.44 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 2831 1.36 - 1.55: 5959 1.55 - 1.73: 0 1.73 - 1.92: 99 1.92 - 2.10: 1 Bond restraints: 8890 Sorted by residual: bond pdb=" C SER A 6 " pdb=" O SER A 6 " ideal model delta sigma weight residual 1.234 1.305 -0.071 1.35e-02 5.49e+03 2.77e+01 bond pdb=" C ASP A 200 " pdb=" O ASP A 200 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.22e-02 6.72e+03 2.67e+01 bond pdb=" C PHE A 307 " pdb=" O PHE A 307 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.19e-02 7.06e+03 2.19e+01 bond pdb=" N VAL R 170 " pdb=" CA VAL R 170 " ideal model delta sigma weight residual 1.459 1.498 -0.039 9.10e-03 1.21e+04 1.87e+01 bond pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta sigma weight residual 1.528 1.462 0.066 1.61e-02 3.86e+03 1.69e+01 ... (remaining 8885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10006 1.89 - 3.78: 1844 3.78 - 5.66: 168 5.66 - 7.55: 17 7.55 - 9.44: 6 Bond angle restraints: 12041 Sorted by residual: angle pdb=" N ILE R 248 " pdb=" CA ILE R 248 " pdb=" C ILE R 248 " ideal model delta sigma weight residual 110.42 100.98 9.44 9.60e-01 1.09e+00 9.67e+01 angle pdb=" N LYS A 210 " pdb=" CA LYS A 210 " pdb=" C LYS A 210 " ideal model delta sigma weight residual 112.92 103.60 9.32 1.23e+00 6.61e-01 5.74e+01 angle pdb=" N LEU A 268 " pdb=" CA LEU A 268 " pdb=" C LEU A 268 " ideal model delta sigma weight residual 108.54 100.39 8.15 1.41e+00 5.03e-01 3.34e+01 angle pdb=" C ASP R 255 " pdb=" N GLY R 256 " pdb=" CA GLY R 256 " ideal model delta sigma weight residual 122.27 116.74 5.53 9.90e-01 1.02e+00 3.12e+01 angle pdb=" CA ARG B 52 " pdb=" C ARG B 52 " pdb=" O ARG B 52 " ideal model delta sigma weight residual 121.58 115.15 6.43 1.16e+00 7.43e-01 3.07e+01 ... (remaining 12036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.67: 5132 30.67 - 61.35: 139 61.35 - 92.02: 7 92.02 - 122.70: 0 122.70 - 153.37: 4 Dihedral angle restraints: 5282 sinusoidal: 2077 harmonic: 3205 Sorted by residual: dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual 93.00 19.91 73.09 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CD ARG B 137 " pdb=" NE ARG B 137 " pdb=" CZ ARG B 137 " pdb=" NH1 ARG B 137 " ideal model delta sinusoidal sigma weight residual 0.00 51.93 -51.93 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 0.00 29.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 5279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 497 0.051 - 0.103: 497 0.103 - 0.154: 272 0.154 - 0.206: 89 0.206 - 0.257: 22 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CB VAL R 234 " pdb=" CA VAL R 234 " pdb=" CG1 VAL R 234 " pdb=" CG2 VAL R 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE R 98 " pdb=" CA ILE R 98 " pdb=" CG1 ILE R 98 " pdb=" CG2 ILE R 98 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1374 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 XS0 R 801 " 0.173 2.00e-02 2.50e+03 7.77e-02 1.81e+02 pdb=" C11 XS0 R 801 " -0.016 2.00e-02 2.50e+03 pdb=" C13 XS0 R 801 " -0.081 2.00e-02 2.50e+03 pdb=" C14 XS0 R 801 " -0.010 2.00e-02 2.50e+03 pdb=" C16 XS0 R 801 " -0.017 2.00e-02 2.50e+03 pdb=" C18 XS0 R 801 " -0.080 2.00e-02 2.50e+03 pdb=" N10 XS0 R 801 " -0.032 2.00e-02 2.50e+03 pdb=" N12 XS0 R 801 " -0.045 2.00e-02 2.50e+03 pdb=" N15 XS0 R 801 " 0.006 2.00e-02 2.50e+03 pdb=" N17 XS0 R 801 " -0.067 2.00e-02 2.50e+03 pdb=" N20 XS0 R 801 " 0.143 2.00e-02 2.50e+03 pdb="CL19 XS0 R 801 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " -0.856 9.50e-02 1.11e+02 3.84e-01 8.93e+01 pdb=" NE ARG B 137 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 205 " -0.726 9.50e-02 1.11e+02 3.25e-01 6.45e+01 pdb=" NE ARG A 205 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 205 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 205 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 205 " -0.024 2.00e-02 2.50e+03 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1312 2.76 - 3.31: 8871 3.31 - 3.86: 14990 3.86 - 4.41: 18911 4.41 - 4.96: 31539 Nonbonded interactions: 75623 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" OD1 ASP B 290 " model vdw 2.215 3.040 nonbonded pdb=" O MET G 21 " pdb=" CG1 ILE G 25 " model vdw 2.238 3.440 nonbonded pdb=" O LEU A 249 " pdb=" OG SER A 252 " model vdw 2.255 3.040 nonbonded pdb=" O GLY B 162 " pdb=" OD1 ASP B 186 " model vdw 2.258 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.279 3.040 ... (remaining 75618 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 21.930 Find NCS groups from input model: 0.080 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4927 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 : 0.012 0.071 8890 Z= 0.810 Angle : 1.430 9.438 12041 Z= 1.034 Chirality : 0.092 0.257 1377 Planarity : 0.028 0.384 1501 Dihedral : 14.434 153.370 3202 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 0.94 % Allowed : 6.82 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.23), residues: 1086 helix: -0.85 (0.24), residues: 374 sheet: -1.81 (0.30), residues: 239 loop : -1.92 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP S 36 HIS 0.013 0.003 HIS A 188 PHE 0.081 0.006 PHE A 199 TYR 0.039 0.005 TYR R 15 ARG 0.011 0.002 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 289 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 308 LEU cc_start: 0.7028 (mt) cc_final: 0.6653 (mt) REVERT: G 55 PRO cc_start: 0.5700 (Cg_exo) cc_final: 0.5484 (Cg_endo) outliers start: 9 outliers final: 2 residues processed: 294 average time/residue: 0.2399 time to fit residues: 93.8240 Evaluate side-chains 170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 119 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 91 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS A 22 ASN A 52 GLN A 213 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8890 Z= 0.224 Angle : 0.702 14.127 12041 Z= 0.371 Chirality : 0.044 0.169 1377 Planarity : 0.005 0.042 1501 Dihedral : 9.336 131.046 1223 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.83 % Allowed : 16.05 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.24), residues: 1086 helix: 0.50 (0.25), residues: 380 sheet: -1.27 (0.30), residues: 276 loop : -1.74 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 128 HIS 0.007 0.001 HIS A 188 PHE 0.012 0.002 PHE A 196 TYR 0.015 0.002 TYR B 105 ARG 0.007 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 MET cc_start: 0.3929 (mmp) cc_final: 0.3611 (mmp) REVERT: S 93 MET cc_start: 0.5498 (mpp) cc_final: 0.5279 (ptp) REVERT: S 218 MET cc_start: 0.4404 (ttp) cc_final: 0.4102 (tmm) REVERT: A 247 MET cc_start: 0.5473 (mmm) cc_final: 0.5184 (mmt) outliers start: 27 outliers final: 11 residues processed: 220 average time/residue: 0.2210 time to fit residues: 65.9143 Evaluate side-chains 172 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain A residue 276 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 176 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN S 159 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 HIS ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8890 Z= 0.256 Angle : 0.754 21.201 12041 Z= 0.389 Chirality : 0.044 0.190 1377 Planarity : 0.005 0.073 1501 Dihedral : 7.542 87.285 1222 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.15 % Allowed : 19.10 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.90 (0.25), residues: 1086 helix: 0.70 (0.26), residues: 375 sheet: -1.06 (0.30), residues: 290 loop : -1.31 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 128 HIS 0.010 0.002 HIS G 44 PHE 0.016 0.002 PHE B 199 TYR 0.019 0.002 TYR B 105 ARG 0.006 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.7287 (t0) cc_final: 0.7036 (t0) REVERT: S 148 ARG cc_start: 0.6280 (mtm-85) cc_final: 0.6011 (mtm-85) REVERT: R 85 PHE cc_start: 0.5503 (m-80) cc_final: 0.5231 (m-10) REVERT: R 99 MET cc_start: 0.6592 (mmp) cc_final: 0.6225 (mmm) REVERT: A 247 MET cc_start: 0.6270 (mmm) cc_final: 0.6019 (mmt) outliers start: 30 outliers final: 19 residues processed: 190 average time/residue: 0.2121 time to fit residues: 55.4645 Evaluate side-chains 171 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 175 TYR Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain A residue 273 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 130 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5534 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8890 Z= 0.180 Angle : 0.691 16.027 12041 Z= 0.355 Chirality : 0.043 0.191 1377 Planarity : 0.004 0.039 1501 Dihedral : 6.004 59.586 1220 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.57 % Allowed : 18.57 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1086 helix: 1.04 (0.26), residues: 369 sheet: -0.87 (0.31), residues: 288 loop : -1.22 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.005 0.001 HIS R 95 PHE 0.014 0.001 PHE R 288 TYR 0.013 0.001 TYR R 118 ARG 0.004 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.7123 (tpp) cc_final: 0.6915 (tpp) REVERT: B 234 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6380 (m-80) REVERT: G 38 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6882 (ttt) REVERT: S 103 TYR cc_start: 0.6091 (t80) cc_final: 0.5843 (t80) REVERT: R 99 MET cc_start: 0.6545 (mmp) cc_final: 0.6256 (mmm) REVERT: R 275 MET cc_start: 0.6993 (tmm) cc_final: 0.6637 (tmm) REVERT: A 247 MET cc_start: 0.6190 (mmm) cc_final: 0.5855 (mmt) outliers start: 34 outliers final: 22 residues processed: 187 average time/residue: 0.2231 time to fit residues: 57.8158 Evaluate side-chains 173 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8890 Z= 0.205 Angle : 0.686 14.875 12041 Z= 0.353 Chirality : 0.043 0.163 1377 Planarity : 0.004 0.042 1501 Dihedral : 5.150 57.989 1220 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.04 % Allowed : 20.15 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1086 helix: 1.17 (0.26), residues: 369 sheet: -0.68 (0.32), residues: 281 loop : -1.06 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 47 HIS 0.005 0.001 HIS B 54 PHE 0.024 0.002 PHE R 288 TYR 0.018 0.002 TYR B 105 ARG 0.009 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.7179 (tpp) cc_final: 0.6842 (tpp) REVERT: B 234 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6206 (m-80) REVERT: R 85 PHE cc_start: 0.4699 (OUTLIER) cc_final: 0.4434 (m-10) REVERT: R 99 MET cc_start: 0.6785 (mmp) cc_final: 0.6474 (mmm) outliers start: 29 outliers final: 18 residues processed: 178 average time/residue: 0.2037 time to fit residues: 50.4459 Evaluate side-chains 164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.0970 chunk 34 optimal weight: 0.1980 chunk 55 optimal weight: 0.0770 chunk 101 optimal weight: 0.5980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.7318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8890 Z= 0.166 Angle : 0.675 12.566 12041 Z= 0.346 Chirality : 0.043 0.199 1377 Planarity : 0.004 0.042 1501 Dihedral : 4.835 55.958 1220 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.04 % Allowed : 21.41 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1086 helix: 1.37 (0.27), residues: 367 sheet: -0.54 (0.32), residues: 280 loop : -0.99 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 128 HIS 0.005 0.001 HIS R 95 PHE 0.016 0.001 PHE R 288 TYR 0.011 0.001 TYR B 105 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.7025 (tpp) cc_final: 0.6735 (tpp) REVERT: B 230 ASN cc_start: 0.5100 (OUTLIER) cc_final: 0.4881 (m-40) REVERT: B 234 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.6104 (m-80) REVERT: B 284 LEU cc_start: 0.6994 (tt) cc_final: 0.6714 (mm) REVERT: S 34 MET cc_start: 0.4593 (mtm) cc_final: 0.4343 (mtt) REVERT: R 99 MET cc_start: 0.6629 (mmp) cc_final: 0.6394 (mmm) REVERT: R 173 MET cc_start: 0.4526 (mmm) cc_final: 0.4238 (mmp) REVERT: R 277 ASN cc_start: 0.5929 (OUTLIER) cc_final: 0.5665 (m-40) REVERT: A 247 MET cc_start: 0.6109 (mmt) cc_final: 0.5396 (mmt) outliers start: 29 outliers final: 18 residues processed: 175 average time/residue: 0.2037 time to fit residues: 49.5522 Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.8466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8890 Z= 0.402 Angle : 0.870 14.369 12041 Z= 0.455 Chirality : 0.050 0.193 1377 Planarity : 0.006 0.070 1501 Dihedral : 6.043 54.663 1220 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.57 % Allowed : 23.19 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1086 helix: 0.31 (0.26), residues: 368 sheet: -0.91 (0.31), residues: 289 loop : -1.03 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 211 HIS 0.007 0.002 HIS S 35 PHE 0.031 0.003 PHE R 200 TYR 0.035 0.003 TYR B 105 ARG 0.009 0.001 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: S 103 TYR cc_start: 0.6459 (t80) cc_final: 0.6176 (t80) REVERT: R 275 MET cc_start: 0.6704 (tmm) cc_final: 0.6065 (ttp) outliers start: 34 outliers final: 22 residues processed: 173 average time/residue: 0.2091 time to fit residues: 50.1944 Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain A residue 331 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.8756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8890 Z= 0.254 Angle : 0.776 13.146 12041 Z= 0.398 Chirality : 0.046 0.247 1377 Planarity : 0.004 0.074 1501 Dihedral : 5.341 52.292 1220 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.94 % Allowed : 24.97 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.73 (0.25), residues: 1086 helix: 0.64 (0.26), residues: 366 sheet: -0.97 (0.31), residues: 274 loop : -0.98 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS B 54 PHE 0.020 0.002 PHE R 288 TYR 0.019 0.002 TYR B 105 ARG 0.005 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6694 (m-80) REVERT: S 103 TYR cc_start: 0.6351 (t80) cc_final: 0.6043 (t80) REVERT: S 223 TYR cc_start: 0.4943 (m-80) cc_final: 0.4590 (m-80) REVERT: S 235 LEU cc_start: 0.7137 (tp) cc_final: 0.6151 (tp) REVERT: R 99 MET cc_start: 0.6466 (mmp) cc_final: 0.5795 (mmm) REVERT: R 275 MET cc_start: 0.6526 (tmm) cc_final: 0.5960 (ttp) REVERT: A 247 MET cc_start: 0.6728 (mmt) cc_final: 0.6154 (mmt) outliers start: 28 outliers final: 22 residues processed: 171 average time/residue: 0.2094 time to fit residues: 49.9257 Evaluate side-chains 164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 246 SER Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 256 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 0.0270 chunk 30 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.9217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8890 Z= 0.323 Angle : 0.828 13.397 12041 Z= 0.426 Chirality : 0.048 0.208 1377 Planarity : 0.005 0.068 1501 Dihedral : 5.611 50.642 1220 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.57 % Allowed : 24.45 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1086 helix: 0.43 (0.26), residues: 367 sheet: -1.13 (0.31), residues: 269 loop : -1.07 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.006 0.002 HIS B 225 PHE 0.020 0.002 PHE R 200 TYR 0.023 0.002 TYR B 105 ARG 0.005 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: B 263 THR cc_start: 0.8197 (t) cc_final: 0.7954 (t) REVERT: S 103 TYR cc_start: 0.6445 (t80) cc_final: 0.6182 (t80) REVERT: S 168 ARG cc_start: 0.7072 (tmm-80) cc_final: 0.6783 (ptt90) REVERT: R 99 MET cc_start: 0.6626 (mmp) cc_final: 0.6064 (mmm) outliers start: 34 outliers final: 29 residues processed: 170 average time/residue: 0.2129 time to fit residues: 50.1647 Evaluate side-chains 172 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 246 SER Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 284 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 219 GLN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.9300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8890 Z= 0.219 Angle : 0.805 12.389 12041 Z= 0.406 Chirality : 0.047 0.247 1377 Planarity : 0.004 0.066 1501 Dihedral : 5.271 46.260 1220 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.94 % Allowed : 25.50 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.72 (0.26), residues: 1086 helix: 0.63 (0.26), residues: 372 sheet: -0.91 (0.32), residues: 264 loop : -1.03 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 242 HIS 0.005 0.001 HIS B 266 PHE 0.019 0.002 PHE R 167 TYR 0.021 0.001 TYR S 59 ARG 0.005 0.000 ARG S 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: B 270 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7202 (mm) REVERT: R 64 LEU cc_start: 0.6324 (tt) cc_final: 0.6078 (tp) REVERT: R 99 MET cc_start: 0.6296 (mmp) cc_final: 0.5681 (mmm) REVERT: R 183 LEU cc_start: 0.7285 (tp) cc_final: 0.6879 (tp) outliers start: 28 outliers final: 23 residues processed: 168 average time/residue: 0.2031 time to fit residues: 47.3222 Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 246 SER Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain A residue 194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 219 GLN R 30 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.153170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.130830 restraints weight = 27570.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.133656 restraints weight = 16739.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.135854 restraints weight = 12057.415| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.9439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8890 Z= 0.212 Angle : 0.807 12.131 12041 Z= 0.404 Chirality : 0.046 0.216 1377 Planarity : 0.004 0.065 1501 Dihedral : 5.210 49.282 1220 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.94 % Allowed : 25.29 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.58 (0.26), residues: 1086 helix: 0.78 (0.27), residues: 369 sheet: -0.80 (0.32), residues: 261 loop : -1.00 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 184 HIS 0.005 0.001 HIS B 266 PHE 0.027 0.002 PHE B 292 TYR 0.019 0.001 TYR S 59 ARG 0.006 0.000 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2101.74 seconds wall clock time: 39 minutes 7.77 seconds (2347.77 seconds total)