Starting phenix.real_space_refine on Thu Mar 13 06:27:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjl_38400/03_2025/8xjl_38400.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjl_38400/03_2025/8xjl_38400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjl_38400/03_2025/8xjl_38400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjl_38400/03_2025/8xjl_38400.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjl_38400/03_2025/8xjl_38400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjl_38400/03_2025/8xjl_38400.cif" } resolution = 2.77 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= 0.014 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 62 5.16 5 C 5624 2.51 5 N 1513 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8846 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1821 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2171 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UGU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.98, per 1000 atoms: 0.56 Number of scatterers: 8846 At special positions: 0 Unit cell: (105.93, 116.63, 111.28, 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 62 16.00 O 1647 8.00 N 1513 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " 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: 2.03 Conformation dependent library (CDL) restraints added in 970.6 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 40.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.530A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 4.090A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.189A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.683A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 245 removed outlier: 3.508A pdb=" N ASP A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.658A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 4.114A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.630A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 59 removed outlier: 4.044A pdb=" N SER R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN R 56 " --> pdb=" O MET R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 Processing helix chain 'R' and resid 97 through 102 Processing helix chain 'R' and resid 105 through 139 removed outlier: 3.538A pdb=" N SER R 109 " --> pdb=" O ASN R 105 " (cutoff:3.500A) Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 148 through 168 Processing helix chain 'R' and resid 168 through 173 Processing helix chain 'R' and resid 195 through 232 removed outlier: 4.138A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 276 removed outlier: 3.679A pdb=" N TRP R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) Proline residue: R 264 - end of helix removed outlier: 3.613A pdb=" N THR R 268 " --> pdb=" O PRO R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.637A pdb=" N ASN R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 321 removed outlier: 3.626A pdb=" N ASN R 314 " --> pdb=" O ALA R 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.598A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.689A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.800A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.165A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.506A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.253A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.506A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.606A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.682A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.344A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.331A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 178 through 179 486 hydrogen bonds defined for protein. 1365 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: 2.91 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2875 1.34 - 1.46: 2140 1.46 - 1.58: 3915 1.58 - 1.69: 3 1.69 - 1.81: 90 Bond restraints: 9023 Sorted by residual: bond pdb=" C11 UGU R 601 " pdb=" C12 UGU R 601 " ideal model delta sigma weight residual 1.530 1.316 0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C8 UGU R 601 " pdb=" C9 UGU R 601 " ideal model delta sigma weight residual 1.531 1.338 0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" C12 UGU R 601 " pdb=" C8 UGU R 601 " ideal model delta sigma weight residual 1.548 1.694 -0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C10 UGU R 601 " pdb=" C11 UGU R 601 " ideal model delta sigma weight residual 1.550 1.616 -0.066 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C6 UGU R 601 " pdb=" C7 UGU R 601 " ideal model delta sigma weight residual 1.502 1.561 -0.059 2.00e-02 2.50e+03 8.70e+00 ... (remaining 9018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 12194 2.95 - 5.90: 23 5.90 - 8.85: 1 8.85 - 11.80: 1 11.80 - 14.75: 3 Bond angle restraints: 12222 Sorted by residual: angle pdb=" C12 UGU R 601 " pdb=" C13 UGU R 601 " pdb=" C14 UGU R 601 " ideal model delta sigma weight residual 127.73 112.98 14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C5 UGU R 601 " pdb=" C6 UGU R 601 " pdb=" C7 UGU R 601 " ideal model delta sigma weight residual 128.14 113.61 14.53 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C13 UGU R 601 " pdb=" C14 UGU R 601 " pdb=" C15 UGU R 601 " ideal model delta sigma weight residual 126.10 112.83 13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C4 UGU R 601 " pdb=" C5 UGU R 601 " pdb=" C6 UGU R 601 " ideal model delta sigma weight residual 128.19 116.86 11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C11 UGU R 601 " pdb=" C12 UGU R 601 " pdb=" C13 UGU R 601 " ideal model delta sigma weight residual 117.79 110.36 7.43 3.00e+00 1.11e-01 6.13e+00 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.54: 5316 33.54 - 67.07: 47 67.07 - 100.61: 4 100.61 - 134.15: 0 134.15 - 167.68: 1 Dihedral angle restraints: 5368 sinusoidal: 2073 harmonic: 3295 Sorted by residual: dihedral pdb=" C16 UGU R 601 " pdb=" C17 UGU R 601 " pdb=" C18 UGU R 601 " pdb=" C19 UGU R 601 " ideal model delta sinusoidal sigma weight residual 297.02 129.34 167.68 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PHE E 31 " pdb=" C PHE E 31 " pdb=" N GLY E 32 " pdb=" CA GLY E 32 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1276 0.068 - 0.136: 118 0.136 - 0.204: 2 0.204 - 0.272: 1 0.272 - 0.340: 1 Chirality restraints: 1398 Sorted by residual: chirality pdb=" C12 UGU R 601 " pdb=" C11 UGU R 601 " pdb=" C13 UGU R 601 " pdb=" C8 UGU R 601 " both_signs ideal model delta sigma weight residual False 2.42 2.76 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C9 UGU R 601 " pdb=" C10 UGU R 601 " pdb=" C8 UGU R 601 " pdb=" O3 UGU R 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.46 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C8 UGU R 601 " pdb=" C12 UGU R 601 " pdb=" C7 UGU R 601 " pdb=" C9 UGU R 601 " both_signs ideal model delta sigma weight residual False -2.54 -2.73 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1395 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 194 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 59 " 0.017 5.00e-02 4.00e+02 2.53e-02 1.03e+00 pdb=" N PRO C 60 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.014 5.00e-02 4.00e+02 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1379 2.76 - 3.30: 8377 3.30 - 3.83: 14805 3.83 - 4.37: 18525 4.37 - 4.90: 31741 Nonbonded interactions: 74827 Sorted by model distance: nonbonded pdb=" O ARG R 291 " pdb=" CG2 THR R 294 " model vdw 2.225 3.460 nonbonded pdb=" O VAL R 303 " pdb=" NH2 ARG R 308 " model vdw 2.270 3.120 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.280 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.283 3.040 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ALA A 218 " model vdw 2.286 3.120 ... (remaining 74822 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: 0.430 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.004 0.214 9023 Z= 0.287 Angle : 0.477 14.755 12222 Z= 0.223 Chirality : 0.041 0.340 1398 Planarity : 0.003 0.043 1548 Dihedral : 10.361 167.683 3231 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.05 % Allowed : 3.38 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1122 helix: 1.35 (0.25), residues: 414 sheet: 1.07 (0.33), residues: 267 loop : 0.37 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.001 PHE B 151 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 0.973 Fit side-chains REVERT: E 42 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7808 (mmtp) REVERT: E 140 MET cc_start: 0.8395 (mmm) cc_final: 0.8174 (mmp) REVERT: E 210 THR cc_start: 0.8082 (p) cc_final: 0.7849 (p) REVERT: R 57 ARG cc_start: 0.7428 (ttm170) cc_final: 0.7096 (mtm-85) REVERT: R 198 ASP cc_start: 0.8000 (t0) cc_final: 0.7693 (t0) outliers start: 10 outliers final: 3 residues processed: 218 average time/residue: 1.2924 time to fit residues: 299.3463 Evaluate side-chains 144 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain R residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 244 ASN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN R 143 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121127 restraints weight = 10261.580| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.73 r_work: 0.3186 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9023 Z= 0.202 Angle : 0.522 6.521 12222 Z= 0.283 Chirality : 0.042 0.145 1398 Planarity : 0.004 0.044 1548 Dihedral : 6.771 130.712 1270 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.95 % Allowed : 11.18 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.26), residues: 1122 helix: 2.68 (0.24), residues: 411 sheet: 1.03 (0.32), residues: 263 loop : 0.46 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 295 HIS 0.005 0.001 HIS R 81 PHE 0.014 0.001 PHE R 101 TYR 0.016 0.001 TYR E 190 ARG 0.005 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.916 Fit side-chains REVERT: A 132 ARG cc_start: 0.7751 (tpt90) cc_final: 0.7364 (tpm170) REVERT: A 183 ASP cc_start: 0.7976 (t70) cc_final: 0.7724 (t70) REVERT: A 230 ASP cc_start: 0.7702 (m-30) cc_final: 0.7411 (m-30) REVERT: E 42 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7793 (mmtp) REVERT: E 45 GLU cc_start: 0.7757 (pt0) cc_final: 0.7536 (pt0) REVERT: E 64 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7751 (tttm) REVERT: E 140 MET cc_start: 0.8419 (mmm) cc_final: 0.8142 (mmp) REVERT: R 285 THR cc_start: 0.6992 (m) cc_final: 0.6708 (p) outliers start: 28 outliers final: 12 residues processed: 165 average time/residue: 1.2035 time to fit residues: 211.7976 Evaluate side-chains 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 139 LYS Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 71 optimal weight: 0.0570 chunk 69 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 119 GLN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121019 restraints weight = 10429.988| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.78 r_work: 0.3179 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9023 Z= 0.191 Angle : 0.506 6.665 12222 Z= 0.268 Chirality : 0.041 0.133 1398 Planarity : 0.004 0.044 1548 Dihedral : 5.970 95.044 1268 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.64 % Allowed : 12.55 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.26), residues: 1122 helix: 2.89 (0.24), residues: 414 sheet: 0.82 (0.31), residues: 273 loop : 0.45 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR R 188 ARG 0.006 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.967 Fit side-chains REVERT: A 222 GLU cc_start: 0.7459 (tt0) cc_final: 0.7253 (tp30) REVERT: C 28 ILE cc_start: 0.8416 (pt) cc_final: 0.8022 (tt) REVERT: E 42 LYS cc_start: 0.8319 (mmtm) cc_final: 0.8038 (mmtp) REVERT: E 64 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7796 (tttm) REVERT: E 140 MET cc_start: 0.8391 (mmm) cc_final: 0.8128 (mmp) REVERT: R 84 ASN cc_start: 0.7741 (m-40) cc_final: 0.7478 (m110) REVERT: R 285 THR cc_start: 0.7073 (m) cc_final: 0.6858 (p) outliers start: 25 outliers final: 15 residues processed: 147 average time/residue: 1.1914 time to fit residues: 187.0897 Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 139 LYS Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 71 optimal weight: 0.0170 chunk 30 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 0.0070 chunk 46 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 119 GLN A 209 HIS B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122527 restraints weight = 10262.159| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.78 r_work: 0.3180 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9023 Z= 0.117 Angle : 0.447 6.102 12222 Z= 0.239 Chirality : 0.039 0.132 1398 Planarity : 0.003 0.045 1548 Dihedral : 5.362 87.496 1268 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.43 % Allowed : 13.08 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.26), residues: 1122 helix: 3.27 (0.24), residues: 410 sheet: 0.67 (0.31), residues: 276 loop : 0.55 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.021 0.001 PHE R 200 TYR 0.015 0.001 TYR E 190 ARG 0.005 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7147 (mptt) REVERT: A 101 ASN cc_start: 0.7412 (t0) cc_final: 0.7068 (t0) REVERT: A 115 TYR cc_start: 0.8377 (m-80) cc_final: 0.8092 (m-80) REVERT: A 132 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7210 (tpm170) REVERT: B 129 ARG cc_start: 0.7158 (mtp180) cc_final: 0.6902 (ttt90) REVERT: B 197 ARG cc_start: 0.6982 (mpt-90) cc_final: 0.6759 (tpp80) REVERT: B 212 ASP cc_start: 0.8548 (t70) cc_final: 0.8197 (t0) REVERT: C 21 MET cc_start: 0.7101 (mtm) cc_final: 0.6846 (mpm) REVERT: C 28 ILE cc_start: 0.8292 (pt) cc_final: 0.7892 (tt) REVERT: E 42 LYS cc_start: 0.8357 (mmtm) cc_final: 0.8033 (mmtp) REVERT: E 219 LEU cc_start: 0.8622 (tp) cc_final: 0.8202 (mm) REVERT: E 220 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: R 84 ASN cc_start: 0.7508 (m-40) cc_final: 0.7184 (m110) REVERT: R 207 PHE cc_start: 0.7644 (t80) cc_final: 0.7430 (t80) outliers start: 23 outliers final: 7 residues processed: 156 average time/residue: 1.4064 time to fit residues: 234.0759 Evaluate side-chains 137 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 213 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.0060 chunk 95 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN R 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120758 restraints weight = 10341.026| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.69 r_work: 0.3145 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9023 Z= 0.154 Angle : 0.471 7.305 12222 Z= 0.249 Chirality : 0.040 0.132 1398 Planarity : 0.003 0.044 1548 Dihedral : 5.227 78.015 1266 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.22 % Allowed : 14.35 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.26), residues: 1122 helix: 3.23 (0.24), residues: 410 sheet: 0.63 (0.30), residues: 279 loop : 0.51 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.014 0.001 PHE R 200 TYR 0.012 0.001 TYR E 190 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.021 Fit side-chains REVERT: A 73 LYS cc_start: 0.7660 (mtpt) cc_final: 0.7325 (mptt) REVERT: A 101 ASN cc_start: 0.7545 (t0) cc_final: 0.7237 (t0) REVERT: A 230 ASP cc_start: 0.7634 (m-30) cc_final: 0.7369 (m-30) REVERT: C 21 MET cc_start: 0.7101 (mtm) cc_final: 0.6829 (mpm) REVERT: C 28 ILE cc_start: 0.8163 (pt) cc_final: 0.7775 (tt) REVERT: E 42 LYS cc_start: 0.8367 (mmtm) cc_final: 0.8034 (mmtp) REVERT: E 220 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: R 84 ASN cc_start: 0.7661 (m-40) cc_final: 0.7283 (m110) REVERT: R 207 PHE cc_start: 0.7640 (t80) cc_final: 0.7429 (t80) outliers start: 21 outliers final: 12 residues processed: 141 average time/residue: 1.2500 time to fit residues: 188.4989 Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 139 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 0.0040 chunk 72 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117971 restraints weight = 10257.719| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.75 r_work: 0.3103 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9023 Z= 0.220 Angle : 0.511 7.712 12222 Z= 0.272 Chirality : 0.041 0.137 1398 Planarity : 0.003 0.043 1548 Dihedral : 5.455 76.891 1266 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.74 % Allowed : 14.77 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.25), residues: 1122 helix: 2.94 (0.24), residues: 420 sheet: 0.53 (0.30), residues: 282 loop : 0.39 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 96 HIS 0.004 0.001 HIS A 82 PHE 0.012 0.002 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7350 (mptt) REVERT: A 101 ASN cc_start: 0.7821 (t0) cc_final: 0.7543 (t0) REVERT: A 230 ASP cc_start: 0.7706 (m-30) cc_final: 0.7447 (m-30) REVERT: C 21 MET cc_start: 0.7183 (mtm) cc_final: 0.6893 (mpm) REVERT: C 28 ILE cc_start: 0.8208 (pt) cc_final: 0.7808 (tt) REVERT: E 42 LYS cc_start: 0.8391 (mmtm) cc_final: 0.8053 (mmtp) REVERT: E 73 ASP cc_start: 0.7999 (m-30) cc_final: 0.7757 (m-30) REVERT: E 220 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: R 207 PHE cc_start: 0.7634 (t80) cc_final: 0.7412 (t80) outliers start: 26 outliers final: 15 residues processed: 146 average time/residue: 1.2881 time to fit residues: 201.2172 Evaluate side-chains 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 139 LYS Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117780 restraints weight = 10360.528| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.74 r_work: 0.3105 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9023 Z= 0.384 Angle : 0.617 8.282 12222 Z= 0.327 Chirality : 0.045 0.155 1398 Planarity : 0.004 0.039 1548 Dihedral : 5.996 80.821 1266 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.95 % Allowed : 14.98 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1122 helix: 2.46 (0.24), residues: 415 sheet: 0.51 (0.30), residues: 266 loop : 0.09 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 96 HIS 0.006 0.002 HIS A 82 PHE 0.017 0.002 PHE E 26 TYR 0.023 0.002 TYR R 188 ARG 0.004 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.090 Fit side-chains REVERT: A 73 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7517 (mptt) REVERT: A 101 ASN cc_start: 0.7957 (t0) cc_final: 0.7716 (t0) REVERT: A 183 ASP cc_start: 0.7960 (t70) cc_final: 0.7685 (t70) REVERT: C 21 MET cc_start: 0.7133 (mtm) cc_final: 0.6883 (mpm) REVERT: C 28 ILE cc_start: 0.8368 (pt) cc_final: 0.7948 (tt) REVERT: E 42 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8069 (mmtp) REVERT: E 73 ASP cc_start: 0.8099 (m-30) cc_final: 0.7884 (m-30) REVERT: R 207 PHE cc_start: 0.7546 (t80) cc_final: 0.7334 (t80) outliers start: 28 outliers final: 15 residues processed: 141 average time/residue: 1.3579 time to fit residues: 203.4199 Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118796 restraints weight = 10460.739| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.79 r_work: 0.3121 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9023 Z= 0.156 Angle : 0.495 6.662 12222 Z= 0.263 Chirality : 0.040 0.133 1398 Planarity : 0.003 0.046 1548 Dihedral : 5.620 78.700 1266 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.48 % Allowed : 16.88 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1122 helix: 3.02 (0.24), residues: 405 sheet: 0.46 (0.30), residues: 276 loop : 0.26 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR E 190 ARG 0.003 0.000 ARG R 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7386 (mptt) REVERT: A 101 ASN cc_start: 0.7799 (t0) cc_final: 0.7440 (t0) REVERT: A 183 ASP cc_start: 0.7903 (t70) cc_final: 0.7537 (t70) REVERT: C 21 MET cc_start: 0.7224 (mtm) cc_final: 0.6881 (mpm) REVERT: C 28 ILE cc_start: 0.8222 (pt) cc_final: 0.7808 (tt) REVERT: E 42 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8029 (mmtp) REVERT: E 73 ASP cc_start: 0.8087 (m-30) cc_final: 0.7870 (m-30) REVERT: E 112 GLN cc_start: 0.8273 (mm-40) cc_final: 0.8062 (mm110) REVERT: R 207 PHE cc_start: 0.7658 (t80) cc_final: 0.7425 (t80) outliers start: 14 outliers final: 12 residues processed: 142 average time/residue: 1.2463 time to fit residues: 188.3433 Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8029 > 50: distance: 81 - 215: 11.280 distance: 118 - 219: 24.001 distance: 121 - 216: 6.583 distance: 143 - 198: 3.319 distance: 181 - 186: 17.297 distance: 186 - 187: 16.109 distance: 186 - 318: 14.217 distance: 187 - 188: 9.010 distance: 187 - 190: 5.946 distance: 188 - 189: 9.883 distance: 188 - 198: 4.586 distance: 189 - 315: 9.049 distance: 190 - 191: 4.718 distance: 191 - 192: 4.321 distance: 191 - 193: 12.541 distance: 192 - 194: 11.176 distance: 193 - 195: 4.140 distance: 194 - 196: 6.885 distance: 195 - 196: 10.017 distance: 196 - 197: 3.917 distance: 198 - 199: 7.959 distance: 199 - 200: 11.359 distance: 199 - 202: 13.662 distance: 200 - 201: 5.183 distance: 200 - 210: 6.029 distance: 202 - 203: 3.247 distance: 203 - 204: 26.863 distance: 203 - 205: 22.433 distance: 204 - 206: 9.180 distance: 205 - 207: 11.168 distance: 206 - 208: 24.364 distance: 207 - 208: 17.253 distance: 208 - 209: 30.969 distance: 211 - 212: 14.855 distance: 211 - 214: 6.667 distance: 212 - 213: 13.260 distance: 212 - 216: 14.965 distance: 214 - 215: 10.506 distance: 217 - 218: 3.052 distance: 217 - 220: 4.522 distance: 218 - 219: 17.217 distance: 218 - 224: 10.698 distance: 220 - 221: 4.924 distance: 221 - 222: 6.386 distance: 222 - 223: 8.591 distance: 224 - 225: 3.551 distance: 225 - 226: 10.020 distance: 225 - 228: 4.916 distance: 226 - 227: 15.821 distance: 226 - 233: 15.116 distance: 228 - 229: 10.059 distance: 229 - 230: 7.442 distance: 230 - 232: 7.007 distance: 233 - 234: 5.069 distance: 234 - 235: 8.874 distance: 234 - 237: 5.836 distance: 235 - 236: 15.922 distance: 235 - 243: 14.131 distance: 237 - 238: 8.109 distance: 238 - 239: 10.244 distance: 238 - 240: 3.017 distance: 239 - 241: 10.968 distance: 240 - 242: 11.175 distance: 241 - 242: 5.732 distance: 243 - 244: 3.499 distance: 244 - 245: 12.866 distance: 244 - 247: 10.880 distance: 245 - 246: 27.604 distance: 245 - 251: 8.025 distance: 247 - 248: 8.506 distance: 248 - 249: 10.744 distance: 248 - 250: 7.312 distance: 251 - 252: 6.125 distance: 252 - 253: 13.727 distance: 252 - 255: 10.636 distance: 253 - 254: 5.802 distance: 253 - 260: 31.453 distance: 255 - 256: 10.517 distance: 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