Starting phenix.real_space_refine on Fri Jul 19 18:21:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/07_2024/8xjl_38400.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/07_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_38400/07_2024/8xjl_38400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/07_2024/8xjl_38400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/07_2024/8xjl_38400.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/07_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 Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.40, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.7 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: 0.87 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: 2.66 Time building geometry restraints manager: 3.97 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: 100.13 - 106.90: 200 106.90 - 113.68: 5020 113.68 - 120.45: 3335 120.45 - 127.23: 3575 127.23 - 134.01: 92 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 2.520 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.280 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.283 2.440 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ALA A 218 " model vdw 2.286 2.520 ... (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 ========== 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: 0.290 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 27.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- 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 : 1.038 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: 1.2162 time to fit residues: 281.6931 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 244 ASN B 88 ASN ** 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: 0.7844 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9023 Z= 0.187 Angle : 0.496 6.435 12222 Z= 0.270 Chirality : 0.041 0.136 1398 Planarity : 0.004 0.044 1548 Dihedral : 6.684 128.380 1270 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.85 % Allowed : 11.39 % Favored : 85.76 % 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: 2.14 (0.26), residues: 1122 helix: 2.76 (0.24), residues: 407 sheet: 1.06 (0.32), residues: 263 loop : 0.47 (0.31), residues: 452 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 0.013 0.001 PHE R 101 TYR 0.015 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 177 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.126 Fit side-chains REVERT: B 175 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: E 42 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7799 (mmtp) REVERT: E 45 GLU cc_start: 0.7550 (pt0) cc_final: 0.7327 (pt0) REVERT: E 64 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7675 (tttm) REVERT: E 140 MET cc_start: 0.8409 (mmm) cc_final: 0.8104 (mmp) outliers start: 27 outliers final: 10 residues processed: 163 average time/residue: 1.2147 time to fit residues: 211.2499 Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 175 GLN 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 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2236 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= 0.168 Angle : 0.477 6.252 12222 Z= 0.253 Chirality : 0.040 0.133 1398 Planarity : 0.003 0.045 1548 Dihedral : 6.194 104.137 1270 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.06 % Allowed : 12.03 % 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: 3.02 (0.24), residues: 412 sheet: 0.85 (0.32), residues: 263 loop : 0.47 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 81 PHE 0.015 0.001 PHE R 90 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 169 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 0.950 Fit side-chains REVERT: A 132 ARG cc_start: 0.7570 (tpt90) cc_final: 0.7283 (tpm170) REVERT: B 138 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7395 (mt-10) REVERT: C 28 ILE cc_start: 0.8402 (pt) cc_final: 0.8078 (tt) REVERT: E 45 GLU cc_start: 0.7565 (pt0) cc_final: 0.7334 (pt0) REVERT: E 140 MET cc_start: 0.8399 (mmm) cc_final: 0.8104 (mmp) outliers start: 29 outliers final: 16 residues processed: 156 average time/residue: 1.1659 time to fit residues: 194.2929 Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 5 ASP 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 11 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9023 Z= 0.148 Angle : 0.463 6.485 12222 Z= 0.245 Chirality : 0.040 0.135 1398 Planarity : 0.003 0.045 1548 Dihedral : 5.242 74.033 1270 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.27 % Allowed : 12.97 % 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: 2.28 (0.26), residues: 1122 helix: 3.08 (0.24), residues: 414 sheet: 0.75 (0.31), residues: 270 loop : 0.56 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.021 0.001 PHE R 200 TYR 0.014 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 167 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7571 (tpt90) cc_final: 0.7279 (tpm170) REVERT: B 138 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7433 (mt-10) REVERT: B 212 ASP cc_start: 0.8263 (t70) cc_final: 0.8006 (t0) REVERT: C 28 ILE cc_start: 0.8378 (pt) cc_final: 0.8039 (tt) REVERT: E 140 MET cc_start: 0.8390 (mmm) cc_final: 0.8106 (mmp) REVERT: R 141 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8452 (mt) REVERT: R 207 PHE cc_start: 0.7639 (t80) cc_final: 0.7434 (t80) outliers start: 31 outliers final: 15 residues processed: 151 average time/residue: 1.3237 time to fit residues: 212.6697 Evaluate side-chains 142 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 5 ASP 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN R 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 0.034 9023 Z= 0.210 Angle : 0.496 6.417 12222 Z= 0.265 Chirality : 0.041 0.135 1398 Planarity : 0.003 0.045 1548 Dihedral : 5.278 71.279 1268 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.16 % Allowed : 14.24 % Favored : 82.59 % 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: 2.15 (0.26), residues: 1122 helix: 2.96 (0.24), residues: 414 sheet: 0.70 (0.31), residues: 269 loop : 0.48 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 96 HIS 0.004 0.001 HIS A 209 PHE 0.014 0.002 PHE R 200 TYR 0.016 0.001 TYR R 188 ARG 0.005 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 165 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.022 Fit side-chains REVERT: A 101 ASN cc_start: 0.7527 (t0) cc_final: 0.7247 (t0) REVERT: B 138 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 28 ILE cc_start: 0.8412 (pt) cc_final: 0.8040 (tt) REVERT: E 140 MET cc_start: 0.8399 (mmm) cc_final: 0.8108 (mmp) REVERT: R 141 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8461 (mt) REVERT: R 207 PHE cc_start: 0.7657 (t80) cc_final: 0.7443 (t80) outliers start: 30 outliers final: 15 residues processed: 151 average time/residue: 1.1878 time to fit residues: 191.2668 Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 75 GLN B 259 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9023 Z= 0.322 Angle : 0.573 6.872 12222 Z= 0.303 Chirality : 0.043 0.140 1398 Planarity : 0.004 0.043 1548 Dihedral : 5.670 74.197 1268 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.16 % Allowed : 14.66 % Favored : 82.17 % 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: 1.75 (0.25), residues: 1122 helix: 2.60 (0.24), residues: 415 sheet: 0.61 (0.31), residues: 263 loop : 0.19 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 96 HIS 0.005 0.001 HIS A 209 PHE 0.015 0.002 PHE E 26 TYR 0.020 0.002 TYR R 188 ARG 0.005 0.001 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 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: B 138 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: C 28 ILE cc_start: 0.8444 (pt) cc_final: 0.8090 (tt) REVERT: E 140 MET cc_start: 0.8421 (mmm) cc_final: 0.8113 (mmp) outliers start: 30 outliers final: 14 residues processed: 144 average time/residue: 1.2691 time to fit residues: 195.3437 Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 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 64 LYS 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 303 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 179 GLN R 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9023 Z= 0.151 Angle : 0.472 6.909 12222 Z= 0.251 Chirality : 0.040 0.132 1398 Planarity : 0.003 0.047 1548 Dihedral : 5.259 69.715 1268 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.79 % Allowed : 16.98 % Favored : 81.22 % 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 (0.25), residues: 1122 helix: 3.04 (0.24), residues: 408 sheet: 0.58 (0.31), residues: 263 loop : 0.35 (0.31), residues: 451 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 E 190 ARG 0.004 0.000 ARG R 133 *********************** 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 147 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 101 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7080 (t0) REVERT: B 138 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7476 (mt-10) REVERT: C 28 ILE cc_start: 0.8321 (pt) cc_final: 0.7974 (tt) REVERT: E 140 MET cc_start: 0.8414 (mmm) cc_final: 0.8086 (mmp) outliers start: 17 outliers final: 12 residues processed: 140 average time/residue: 1.3200 time to fit residues: 196.3164 Evaluate side-chains 135 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.0060 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.4914 ------------------------------------------------------------------------------- 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 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9023 Z= 0.131 Angle : 0.461 8.596 12222 Z= 0.243 Chirality : 0.039 0.133 1398 Planarity : 0.003 0.048 1548 Dihedral : 4.999 62.560 1268 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.48 % Allowed : 17.72 % Favored : 80.80 % 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: 2.20 (0.26), residues: 1122 helix: 3.20 (0.25), residues: 404 sheet: 0.61 (0.31), residues: 271 loop : 0.45 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 0.004 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 142 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 101 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.7054 (t0) REVERT: B 46 ARG cc_start: 0.7517 (mmm160) cc_final: 0.7274 (mmm-85) REVERT: B 138 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7462 (mt-10) REVERT: C 28 ILE cc_start: 0.8247 (pt) cc_final: 0.7922 (tt) REVERT: E 140 MET cc_start: 0.8415 (mmm) cc_final: 0.8064 (mmp) outliers start: 14 outliers final: 10 residues processed: 137 average time/residue: 1.3402 time to fit residues: 194.9578 Evaluate side-chains 135 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 158 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 84 ASN R 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9023 Z= 0.189 Angle : 0.492 7.321 12222 Z= 0.260 Chirality : 0.041 0.131 1398 Planarity : 0.003 0.047 1548 Dihedral : 5.159 63.032 1268 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.37 % Allowed : 17.93 % Favored : 80.70 % 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 (0.26), residues: 1122 helix: 3.07 (0.24), residues: 406 sheet: 0.64 (0.30), residues: 274 loop : 0.31 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR B 59 ARG 0.003 0.000 ARG A 225 *********************** 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 133 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 101 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7123 (t0) REVERT: B 46 ARG cc_start: 0.7532 (mmm160) cc_final: 0.7282 (mmm-85) REVERT: C 28 ILE cc_start: 0.8294 (pt) cc_final: 0.7969 (tt) REVERT: E 140 MET cc_start: 0.8452 (mmm) cc_final: 0.8054 (mmp) outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 1.3050 time to fit residues: 175.9261 Evaluate side-chains 131 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 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 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2827 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= 0.163 Angle : 0.491 11.230 12222 Z= 0.257 Chirality : 0.040 0.131 1398 Planarity : 0.003 0.048 1548 Dihedral : 5.116 62.414 1268 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.27 % Allowed : 18.14 % Favored : 80.59 % 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: 2.10 (0.26), residues: 1122 helix: 3.04 (0.24), residues: 408 sheet: 0.66 (0.30), residues: 274 loop : 0.35 (0.32), residues: 440 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 0.014 0.001 TYR B 59 ARG 0.003 0.000 ARG A 225 ********************** 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 134 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 101 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7087 (t0) REVERT: B 46 ARG cc_start: 0.7531 (mmm160) cc_final: 0.7274 (mmm-85) REVERT: C 28 ILE cc_start: 0.8266 (pt) cc_final: 0.7943 (tt) REVERT: E 140 MET cc_start: 0.8425 (mmm) cc_final: 0.8055 (mmp) outliers start: 12 outliers final: 11 residues processed: 129 average time/residue: 1.2846 time to fit residues: 176.0779 Evaluate side-chains 130 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 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 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: 9.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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 18 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 179 GLN R 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117955 restraints weight = 10280.966| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.76 r_work: 0.3139 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9023 Z= 0.387 Angle : 0.610 8.168 12222 Z= 0.323 Chirality : 0.045 0.160 1398 Planarity : 0.004 0.042 1548 Dihedral : 5.865 72.690 1268 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.69 % Allowed : 17.83 % Favored : 80.49 % 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: 1.57 (0.25), residues: 1122 helix: 2.53 (0.24), residues: 405 sheet: 0.48 (0.31), residues: 261 loop : 0.09 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 96 HIS 0.005 0.001 HIS A 209 PHE 0.017 0.002 PHE E 26 TYR 0.021 0.002 TYR B 59 ARG 0.005 0.001 ARG A 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.08 seconds wall clock time: 66 minutes 57.88 seconds (4017.88 seconds total)