Starting phenix.real_space_refine on Tue Sep 24 19:07:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/09_2024/8xjl_38400.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/09_2024/8xjl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/09_2024/8xjl_38400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/09_2024/8xjl_38400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/09_2024/8xjl_38400.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/09_2024/8xjl_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.58, per 1000 atoms: 0.63 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.08 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: 2.71 Time building geometry restraints manager: 2.66 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.560 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:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 0.962 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: 1.2244 time to fit residues: 283.6971 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.119 Fit side-chains REVERT: A 132 ARG cc_start: 0.7536 (tpt90) cc_final: 0.7265 (tpm170) REVERT: A 230 ASP cc_start: 0.7697 (m-30) cc_final: 0.7424 (m-30) REVERT: B 138 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: E 42 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7746 (mmtp) REVERT: E 64 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7717 (tttm) REVERT: E 140 MET cc_start: 0.8431 (mmm) cc_final: 0.8128 (mmp) outliers start: 28 outliers final: 12 residues processed: 165 average time/residue: 1.1707 time to fit residues: 206.2842 Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 138 GLU 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 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2387 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= 0.159 Angle : 0.488 6.543 12222 Z= 0.259 Chirality : 0.040 0.133 1398 Planarity : 0.003 0.044 1548 Dihedral : 5.857 93.002 1268 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.64 % Allowed : 12.45 % Favored : 84.92 % 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: 2.23 (0.26), residues: 1122 helix: 2.99 (0.24), residues: 414 sheet: 0.83 (0.31), residues: 273 loop : 0.51 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 81 PHE 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR E 190 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 165 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.461 Fit side-chains REVERT: C 28 ILE cc_start: 0.8427 (pt) cc_final: 0.8075 (tt) REVERT: E 64 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7713 (tttm) REVERT: E 140 MET cc_start: 0.8422 (mmm) cc_final: 0.8130 (mmp) REVERT: R 84 ASN cc_start: 0.7720 (m-40) cc_final: 0.7482 (m110) outliers start: 25 outliers final: 12 residues processed: 151 average time/residue: 1.1968 time to fit residues: 193.6728 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 216 THR 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 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9023 Z= 0.225 Angle : 0.513 6.603 12222 Z= 0.275 Chirality : 0.041 0.135 1398 Planarity : 0.004 0.044 1548 Dihedral : 5.623 88.026 1266 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.95 % Allowed : 13.29 % Favored : 83.76 % 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: 2.07 (0.26), residues: 1122 helix: 2.84 (0.24), residues: 420 sheet: 0.70 (0.30), residues: 278 loop : 0.41 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 96 HIS 0.006 0.001 HIS A 82 PHE 0.020 0.002 PHE R 200 TYR 0.012 0.001 TYR E 190 ARG 0.004 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 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7555 (mtpt) cc_final: 0.7335 (mptt) REVERT: C 28 ILE cc_start: 0.8412 (pt) cc_final: 0.8080 (tt) REVERT: E 64 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: E 140 MET cc_start: 0.8393 (mmm) cc_final: 0.8120 (mmp) REVERT: E 220 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: R 141 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8524 (mt) outliers start: 28 outliers final: 14 residues processed: 144 average time/residue: 1.0696 time to fit residues: 164.3177 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP 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 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 141 ILE Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.0010 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2581 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 : 0.505 7.408 12222 Z= 0.268 Chirality : 0.041 0.134 1398 Planarity : 0.003 0.045 1548 Dihedral : 5.548 84.418 1266 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.74 % Allowed : 14.03 % Favored : 83.23 % 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: 2.04 (0.25), residues: 1122 helix: 2.87 (0.24), residues: 420 sheet: 0.65 (0.30), residues: 278 loop : 0.37 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.015 0.001 PHE R 200 TYR 0.017 0.001 TYR R 188 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 155 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.193 Fit side-chains REVERT: A 73 LYS cc_start: 0.7584 (mtpt) cc_final: 0.7286 (mptt) REVERT: C 28 ILE cc_start: 0.8390 (pt) cc_final: 0.8051 (tt) REVERT: E 140 MET cc_start: 0.8401 (mmm) cc_final: 0.8115 (mmp) REVERT: E 219 LEU cc_start: 0.8616 (tp) cc_final: 0.8354 (mm) REVERT: E 220 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: R 141 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8463 (mt) outliers start: 26 outliers final: 14 residues processed: 144 average time/residue: 1.1848 time to fit residues: 181.5019 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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 141 ILE Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 75 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 0.035 9023 Z= 0.198 Angle : 0.503 7.314 12222 Z= 0.268 Chirality : 0.041 0.137 1398 Planarity : 0.003 0.045 1548 Dihedral : 5.524 80.663 1266 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.74 % Allowed : 14.14 % Favored : 83.12 % 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: 2.00 (0.25), residues: 1122 helix: 2.90 (0.24), residues: 420 sheet: 0.55 (0.30), residues: 279 loop : 0.32 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.013 0.001 PHE B 199 TYR 0.016 0.001 TYR R 188 ARG 0.004 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 155 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7288 (mptt) REVERT: A 101 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7216 (t0) REVERT: C 28 ILE cc_start: 0.8266 (pt) cc_final: 0.7940 (tt) REVERT: E 140 MET cc_start: 0.8402 (mmm) cc_final: 0.8116 (mmp) REVERT: E 219 LEU cc_start: 0.8560 (tp) cc_final: 0.8325 (mm) REVERT: E 220 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: R 141 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8489 (mt) outliers start: 26 outliers final: 15 residues processed: 142 average time/residue: 1.3318 time to fit residues: 201.0956 Evaluate side-chains 139 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN 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 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 141 ILE Chi-restraints excluded: chain R residue 213 LEU 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 12 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9023 Z= 0.163 Angle : 0.495 8.436 12222 Z= 0.262 Chirality : 0.040 0.133 1398 Planarity : 0.003 0.046 1548 Dihedral : 5.463 78.527 1266 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.32 % Allowed : 15.40 % Favored : 82.28 % 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: 2.06 (0.26), residues: 1122 helix: 3.00 (0.24), residues: 420 sheet: 0.56 (0.30), residues: 279 loop : 0.31 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.013 0.001 PHE B 199 TYR 0.016 0.001 TYR B 59 ARG 0.004 0.000 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 152 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7591 (mtpt) cc_final: 0.7319 (mptt) REVERT: A 101 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.7101 (t0) REVERT: C 28 ILE cc_start: 0.8205 (pt) cc_final: 0.7894 (tt) REVERT: E 140 MET cc_start: 0.8398 (mmm) cc_final: 0.8106 (mmp) REVERT: E 219 LEU cc_start: 0.8534 (tp) cc_final: 0.8300 (mm) REVERT: E 220 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: R 141 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8453 (mt) outliers start: 22 outliers final: 15 residues processed: 143 average time/residue: 1.2834 time to fit residues: 195.3965 Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 217 CYS 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 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 141 ILE Chi-restraints excluded: chain R residue 213 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 64 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9023 Z= 0.158 Angle : 0.480 6.771 12222 Z= 0.255 Chirality : 0.040 0.132 1398 Planarity : 0.003 0.046 1548 Dihedral : 5.357 71.544 1266 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.43 % Allowed : 15.82 % Favored : 81.75 % 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: 2.11 (0.26), residues: 1122 helix: 3.09 (0.24), residues: 415 sheet: 0.58 (0.30), residues: 274 loop : 0.33 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 209 PHE 0.013 0.001 PHE R 101 TYR 0.017 0.001 TYR B 59 ARG 0.004 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 150 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8208 (pt) cc_final: 0.7886 (tt) REVERT: C 47 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: E 140 MET cc_start: 0.8401 (mmm) cc_final: 0.8114 (mmp) REVERT: E 219 LEU cc_start: 0.8544 (tp) cc_final: 0.8296 (mm) REVERT: E 220 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: R 141 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8468 (mt) outliers start: 23 outliers final: 16 residues processed: 140 average time/residue: 1.2159 time to fit residues: 181.4940 Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 C residue 47 GLU 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 141 ILE Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9023 Z= 0.175 Angle : 0.505 10.655 12222 Z= 0.265 Chirality : 0.041 0.133 1398 Planarity : 0.003 0.046 1548 Dihedral : 5.357 68.615 1266 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.22 % Allowed : 16.67 % Favored : 81.12 % 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: 2.08 (0.25), residues: 1122 helix: 3.05 (0.24), residues: 415 sheet: 0.58 (0.30), residues: 273 loop : 0.32 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 209 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG R 133 *********************** REFINEMENT MACRO_CYCLE 9 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 146 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 101 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7075 (t0) REVERT: C 28 ILE cc_start: 0.8215 (pt) cc_final: 0.7892 (tt) REVERT: E 140 MET cc_start: 0.8392 (mmm) cc_final: 0.8097 (mmp) REVERT: E 220 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: R 141 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8451 (mt) outliers start: 21 outliers final: 15 residues processed: 138 average time/residue: 1.2961 time to fit residues: 190.0573 Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 101 ASN 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 B residue 275 SER 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 141 ILE Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9023 Z= 0.156 Angle : 0.480 6.953 12222 Z= 0.255 Chirality : 0.040 0.132 1398 Planarity : 0.003 0.047 1548 Dihedral : 5.264 64.200 1266 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.00 % Allowed : 16.88 % Favored : 81.12 % 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: 3.14 (0.24), residues: 414 sheet: 0.55 (0.30), residues: 273 loop : 0.37 (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 209 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR B 59 ARG 0.004 0.000 ARG R 133 ********************** REFINEMENT MACRO_CYCLE 10 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 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 101 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.7086 (t0) REVERT: B 46 ARG cc_start: 0.7504 (mmm160) cc_final: 0.7251 (mmm-85) REVERT: C 28 ILE cc_start: 0.8186 (pt) cc_final: 0.7883 (tt) REVERT: E 140 MET cc_start: 0.8421 (mmm) cc_final: 0.8131 (mmp) REVERT: E 220 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: R 141 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8448 (mt) outliers start: 19 outliers final: 15 residues processed: 137 average time/residue: 1.3072 time to fit residues: 192.3202 Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 101 ASN 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 B residue 275 SER 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 141 ILE Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.0470 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 0.0770 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 250 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119924 restraints weight = 10258.486| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.75 r_work: 0.3178 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9023 Z= 0.146 Angle : 0.501 11.555 12222 Z= 0.261 Chirality : 0.040 0.155 1398 Planarity : 0.003 0.047 1548 Dihedral : 5.163 58.795 1266 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.90 % Allowed : 17.19 % Favored : 80.91 % 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: 2.17 (0.26), residues: 1122 helix: 3.18 (0.24), residues: 410 sheet: 0.55 (0.30), residues: 273 loop : 0.40 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 209 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR E 190 ARG 0.003 0.000 ARG A 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3745.31 seconds wall clock time: 68 minutes 58.99 seconds (4138.99 seconds total)