Starting phenix.real_space_refine on Tue Mar 11 23:07:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xbw_33107/03_2025/7xbw_33107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xbw_33107/03_2025/7xbw_33107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xbw_33107/03_2025/7xbw_33107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xbw_33107/03_2025/7xbw_33107.map" model { file = "/net/cci-nas-00/data/ceres_data/7xbw_33107/03_2025/7xbw_33107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xbw_33107/03_2025/7xbw_33107.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 42 5.16 5 C 4316 2.51 5 N 1087 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6663 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1657 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2394 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 323} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 352 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2176 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 278} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.35, per 1000 atoms: 0.65 Number of scatterers: 6663 At special positions: 0 Unit cell: (107.635, 111.815, 73.15, 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 42 16.00 O 1218 8.00 N 1087 7.00 C 4316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 916.3 milliseconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 45.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'C' and resid 6 through 32 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.348A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.063A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 327 through 349 removed outlier: 4.333A pdb=" N ASN C 331 " --> pdb=" O THR C 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'E' and resid 10 through 25 removed outlier: 3.686A pdb=" N GLU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 Processing helix chain 'R' and resid 30 through 57 Processing helix chain 'R' and resid 64 through 92 Proline residue: R 85 - end of helix Processing helix chain 'R' and resid 98 through 132 Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 145 through 162 removed outlier: 3.637A pdb=" N ILE R 149 " --> pdb=" O HIS R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 165 No H-bonds generated for 'chain 'R' and resid 163 through 165' Processing helix chain 'R' and resid 180 through 185 removed outlier: 3.838A pdb=" N GLU R 185 " --> pdb=" O GLU R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 201 Processing helix chain 'R' and resid 201 through 221 removed outlier: 3.503A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 259 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 266 through 289 removed outlier: 5.433A pdb=" N ARG R 272 " --> pdb=" O ARG R 268 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 297 removed outlier: 3.960A pdb=" N PHE R 295 " --> pdb=" O LEU R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 310 removed outlier: 3.746A pdb=" N LYS R 310 " --> pdb=" O HIS R 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 53 through 55 removed outlier: 6.418A pdb=" N HIS C 188 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 185 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.737A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 80 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 103 through 105 removed outlier: 5.823A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG D 134 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.678A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.973A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 201 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 203 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.776A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 6.943A pdb=" N VAL D 296 " --> pdb=" O ALA D 305 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.94 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: 2115 1.34 - 1.46: 1643 1.46 - 1.58: 2993 1.58 - 1.70: 4 1.70 - 1.81: 55 Bond restraints: 6810 Sorted by residual: bond pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " ideal model delta sigma weight residual 1.332 1.465 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.464 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 1.332 1.463 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C3 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sigma weight residual 1.413 1.298 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C3 CLR R 401 " pdb=" O1 CLR R 401 " ideal model delta sigma weight residual 1.413 1.299 0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 6805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 9145 1.73 - 3.45: 123 3.45 - 5.18: 36 5.18 - 6.90: 7 6.90 - 8.63: 1 Bond angle restraints: 9312 Sorted by residual: angle pdb=" CA PRO E 60 " pdb=" N PRO E 60 " pdb=" CD PRO E 60 " ideal model delta sigma weight residual 112.00 106.71 5.29 1.40e+00 5.10e-01 1.43e+01 angle pdb=" C TYR R 259 " pdb=" N ASP R 260 " pdb=" CA ASP R 260 " ideal model delta sigma weight residual 122.08 125.76 -3.68 1.47e+00 4.63e-01 6.27e+00 angle pdb=" CA LEU R 84 " pdb=" CB LEU R 84 " pdb=" CG LEU R 84 " ideal model delta sigma weight residual 116.30 124.93 -8.63 3.50e+00 8.16e-02 6.08e+00 angle pdb=" C PRO E 60 " pdb=" CA PRO E 60 " pdb=" CB PRO E 60 " ideal model delta sigma weight residual 110.00 112.72 -2.72 1.12e+00 7.97e-01 5.92e+00 angle pdb=" C PRO C 282 " pdb=" N LEU C 283 " pdb=" CA LEU C 283 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.81e+00 ... (remaining 9307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 3718 14.96 - 29.91: 286 29.91 - 44.87: 82 44.87 - 59.82: 8 59.82 - 74.78: 4 Dihedral angle restraints: 4098 sinusoidal: 1515 harmonic: 2583 Sorted by residual: dihedral pdb=" CA ASP D 170 " pdb=" CB ASP D 170 " pdb=" CG ASP D 170 " pdb=" OD1 ASP D 170 " ideal model delta sinusoidal sigma weight residual -30.00 -81.40 51.40 1 2.00e+01 2.50e-03 9.03e+00 dihedral pdb=" CA CYS R 102 " pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 175 " ideal model delta sinusoidal sigma weight residual 79.00 129.88 -50.88 1 2.00e+01 2.50e-03 8.86e+00 dihedral pdb=" CB ARG D 150 " pdb=" CG ARG D 150 " pdb=" CD ARG D 150 " pdb=" NE ARG D 150 " ideal model delta sinusoidal sigma weight residual 60.00 106.56 -46.56 3 1.50e+01 4.44e-03 8.35e+00 ... (remaining 4095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 858 0.043 - 0.087: 202 0.087 - 0.130: 59 0.130 - 0.173: 5 0.173 - 0.217: 3 Chirality restraints: 1127 Sorted by residual: chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1124 not shown) Planarity restraints: 1155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 38 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO D 39 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 59 " 0.039 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO E 60 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 84 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO R 85 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 85 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 85 " 0.022 5.00e-02 4.00e+02 ... (remaining 1152 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1388 2.78 - 3.31: 6610 3.31 - 3.84: 11485 3.84 - 4.37: 13225 4.37 - 4.90: 23050 Nonbonded interactions: 55758 Sorted by model distance: nonbonded pdb=" OG1 THR D 274 " pdb=" O VAL D 315 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR R 179 " pdb=" NH1 ARG R 191 " model vdw 2.258 3.120 nonbonded pdb=" OG1 THR D 86 " pdb=" OD1 ASN D 88 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP C 200 " pdb=" OG1 THR C 202 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR D 145 " pdb=" OD2 ASP D 186 " model vdw 2.288 3.040 ... (remaining 55753 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: 0.010 Normalize map: mean=0, sd=1: 0.670 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.790 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 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 : 0.005 0.133 6810 Z= 0.286 Angle : 0.542 8.631 9312 Z= 0.271 Chirality : 0.042 0.217 1127 Planarity : 0.004 0.081 1155 Dihedral : 11.689 74.778 2419 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.30), residues: 874 helix: 2.46 (0.27), residues: 382 sheet: 0.54 (0.41), residues: 178 loop : -0.64 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 82 HIS 0.004 0.001 HIS R 285 PHE 0.020 0.001 PHE R 110 TYR 0.019 0.001 TYR R 90 ARG 0.004 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.688 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 1.0452 time to fit residues: 130.7470 Evaluate side-chains 87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN R 248 ASN ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.187215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142181 restraints weight = 6730.928| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.59 r_work: 0.3557 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6810 Z= 0.272 Angle : 0.566 8.856 9312 Z= 0.295 Chirality : 0.042 0.143 1127 Planarity : 0.004 0.061 1155 Dihedral : 4.517 52.652 1125 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.12 % Allowed : 12.86 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.29), residues: 874 helix: 2.13 (0.26), residues: 387 sheet: 0.30 (0.39), residues: 183 loop : -0.60 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 82 HIS 0.007 0.001 HIS R 285 PHE 0.025 0.002 PHE R 110 TYR 0.014 0.002 TYR D 59 ARG 0.004 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.655 Fit side-chains REVERT: C 9 ASP cc_start: 0.6583 (m-30) cc_final: 0.6352 (OUTLIER) REVERT: C 313 ARG cc_start: 0.7372 (mtt90) cc_final: 0.7085 (mtt90) REVERT: D 52 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.8079 (mtt90) REVERT: D 134 ARG cc_start: 0.7959 (ptp-110) cc_final: 0.7728 (ptp-110) REVERT: D 304 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7550 (mtm110) REVERT: R 288 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6106 (pt) outliers start: 14 outliers final: 8 residues processed: 113 average time/residue: 1.0285 time to fit residues: 123.2330 Evaluate side-chains 104 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 ASN ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.184597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136172 restraints weight = 6814.228| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.14 r_work: 0.3524 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6810 Z= 0.224 Angle : 0.531 8.136 9312 Z= 0.279 Chirality : 0.040 0.138 1127 Planarity : 0.004 0.053 1155 Dihedral : 4.565 51.335 1125 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.12 % Allowed : 16.34 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 874 helix: 1.97 (0.26), residues: 392 sheet: 0.09 (0.39), residues: 175 loop : -0.63 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 82 HIS 0.008 0.001 HIS R 285 PHE 0.023 0.002 PHE R 110 TYR 0.020 0.001 TYR R 90 ARG 0.002 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.651 Fit side-chains REVERT: C 306 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7570 (mt0) REVERT: D 196 THR cc_start: 0.6879 (m) cc_final: 0.6573 (p) REVERT: R 288 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6291 (pt) outliers start: 14 outliers final: 6 residues processed: 123 average time/residue: 0.9624 time to fit residues: 126.1007 Evaluate side-chains 104 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.181146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138496 restraints weight = 7025.029| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.98 r_work: 0.3436 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6810 Z= 0.218 Angle : 0.540 11.547 9312 Z= 0.278 Chirality : 0.040 0.136 1127 Planarity : 0.003 0.049 1155 Dihedral : 4.544 55.988 1125 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.78 % Allowed : 18.76 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.28), residues: 874 helix: 1.95 (0.26), residues: 391 sheet: 0.00 (0.38), residues: 180 loop : -0.70 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.008 0.001 HIS R 285 PHE 0.018 0.002 PHE R 110 TYR 0.020 0.001 TYR R 90 ARG 0.002 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.723 Fit side-chains REVERT: C 309 ASP cc_start: 0.7571 (m-30) cc_final: 0.7255 (m-30) REVERT: D 263 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8412 (m) REVERT: D 270 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7727 (pp) REVERT: D 304 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7641 (mtt180) REVERT: R 288 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6371 (pt) outliers start: 25 outliers final: 14 residues processed: 126 average time/residue: 0.9227 time to fit residues: 124.0243 Evaluate side-chains 116 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 304 ARG Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 35 optimal weight: 0.0670 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.182004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140518 restraints weight = 6894.953| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.97 r_work: 0.3482 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6810 Z= 0.195 Angle : 0.536 10.408 9312 Z= 0.278 Chirality : 0.040 0.134 1127 Planarity : 0.003 0.046 1155 Dihedral : 4.390 51.388 1125 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.08 % Allowed : 19.82 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 874 helix: 2.00 (0.26), residues: 391 sheet: -0.17 (0.38), residues: 179 loop : -0.73 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.008 0.001 HIS R 285 PHE 0.025 0.001 PHE R 165 TYR 0.022 0.001 TYR R 90 ARG 0.007 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.694 Fit side-chains REVERT: C 251 ASP cc_start: 0.8204 (t0) cc_final: 0.7989 (t0) REVERT: D 46 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7214 (mmm160) REVERT: D 263 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8426 (m) REVERT: D 304 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7642 (mtt90) REVERT: R 165 PHE cc_start: 0.7180 (p90) cc_final: 0.6963 (p90) REVERT: R 288 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6383 (pt) outliers start: 27 outliers final: 15 residues processed: 121 average time/residue: 0.8992 time to fit residues: 116.3146 Evaluate side-chains 113 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 304 ARG Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 53 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 ASN ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.178119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135433 restraints weight = 6940.308| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.95 r_work: 0.3471 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6810 Z= 0.260 Angle : 0.581 9.611 9312 Z= 0.300 Chirality : 0.041 0.137 1127 Planarity : 0.003 0.044 1155 Dihedral : 4.565 47.854 1125 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.24 % Allowed : 20.88 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.28), residues: 874 helix: 1.88 (0.26), residues: 391 sheet: 0.01 (0.38), residues: 180 loop : -0.81 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.008 0.001 HIS R 285 PHE 0.023 0.002 PHE R 165 TYR 0.021 0.001 TYR R 90 ARG 0.007 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.717 Fit side-chains REVERT: C 276 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: C 309 ASP cc_start: 0.7626 (m-30) cc_final: 0.7322 (m-30) REVERT: D 46 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7399 (mmm160) REVERT: D 270 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7791 (pp) REVERT: R 288 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6467 (pt) outliers start: 28 outliers final: 17 residues processed: 128 average time/residue: 0.9063 time to fit residues: 124.0746 Evaluate side-chains 116 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 0.0370 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 58 optimal weight: 0.0370 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 ASN ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.180478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.139525 restraints weight = 6929.930| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.93 r_work: 0.3455 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6810 Z= 0.197 Angle : 0.562 12.406 9312 Z= 0.287 Chirality : 0.040 0.132 1127 Planarity : 0.003 0.043 1155 Dihedral : 4.443 51.030 1125 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.63 % Allowed : 21.94 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.28), residues: 874 helix: 1.97 (0.26), residues: 391 sheet: -0.21 (0.37), residues: 173 loop : -0.83 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 82 HIS 0.008 0.001 HIS R 285 PHE 0.020 0.001 PHE R 165 TYR 0.023 0.001 TYR R 90 ARG 0.009 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.649 Fit side-chains REVERT: C 251 ASP cc_start: 0.8242 (t0) cc_final: 0.8038 (t0) REVERT: D 46 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7383 (mmm160) REVERT: D 263 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8471 (m) REVERT: D 270 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7759 (pp) REVERT: R 103 LYS cc_start: 0.6819 (ttmm) cc_final: 0.6493 (mmtm) REVERT: R 288 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6558 (pt) outliers start: 24 outliers final: 17 residues processed: 118 average time/residue: 0.9831 time to fit residues: 123.3081 Evaluate side-chains 115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.0370 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.180215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139247 restraints weight = 6962.465| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.97 r_work: 0.3434 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6810 Z= 0.201 Angle : 0.563 11.971 9312 Z= 0.288 Chirality : 0.040 0.131 1127 Planarity : 0.003 0.043 1155 Dihedral : 4.477 54.457 1125 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.24 % Allowed : 21.48 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.28), residues: 874 helix: 1.98 (0.26), residues: 391 sheet: -0.01 (0.37), residues: 178 loop : -0.89 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.008 0.001 HIS R 285 PHE 0.015 0.001 PHE R 165 TYR 0.023 0.001 TYR R 90 ARG 0.009 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: C 251 ASP cc_start: 0.8266 (t0) cc_final: 0.8059 (t0) REVERT: C 276 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: D 46 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7435 (mmm-85) REVERT: D 263 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8486 (m) REVERT: D 270 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7748 (pp) REVERT: R 192 ASN cc_start: 0.7004 (m-40) cc_final: 0.6596 (t0) REVERT: R 207 MET cc_start: 0.7782 (mtm) cc_final: 0.7569 (mtp) REVERT: R 288 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6487 (pt) outliers start: 28 outliers final: 18 residues processed: 121 average time/residue: 0.9249 time to fit residues: 119.5238 Evaluate side-chains 120 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.0060 chunk 8 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 82 optimal weight: 0.0000 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.138347 restraints weight = 6966.263| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.15 r_work: 0.3545 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6810 Z= 0.181 Angle : 0.559 11.451 9312 Z= 0.288 Chirality : 0.040 0.131 1127 Planarity : 0.003 0.044 1155 Dihedral : 4.453 57.313 1125 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.78 % Allowed : 22.84 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.28), residues: 874 helix: 2.01 (0.26), residues: 392 sheet: 0.11 (0.37), residues: 176 loop : -0.92 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 82 HIS 0.007 0.001 HIS R 285 PHE 0.022 0.001 PHE R 165 TYR 0.011 0.001 TYR R 90 ARG 0.011 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: C 276 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6642 (pm20) REVERT: D 46 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7350 (mmm-85) REVERT: D 263 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8467 (m) REVERT: R 103 LYS cc_start: 0.6760 (ttmm) cc_final: 0.6474 (mmtm) REVERT: R 166 MET cc_start: 0.7618 (ptt) cc_final: 0.7265 (ptp) REVERT: R 192 ASN cc_start: 0.7014 (m-40) cc_final: 0.6571 (t0) REVERT: R 207 MET cc_start: 0.7720 (mtm) cc_final: 0.7502 (mtp) REVERT: R 286 CYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8044 (p) REVERT: R 288 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6403 (pt) outliers start: 25 outliers final: 17 residues processed: 115 average time/residue: 0.9688 time to fit residues: 118.5732 Evaluate side-chains 115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN D 237 ASN ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.178326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137119 restraints weight = 7049.598| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.93 r_work: 0.3431 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6810 Z= 0.241 Angle : 0.591 11.204 9312 Z= 0.305 Chirality : 0.041 0.134 1127 Planarity : 0.004 0.047 1155 Dihedral : 4.649 58.854 1125 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.93 % Allowed : 22.69 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 874 helix: 1.95 (0.26), residues: 386 sheet: -0.12 (0.38), residues: 173 loop : -0.91 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 82 HIS 0.007 0.001 HIS R 285 PHE 0.016 0.002 PHE R 165 TYR 0.025 0.001 TYR R 90 ARG 0.011 0.001 ARG C 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: C 276 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: D 46 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7445 (mmm-85) REVERT: R 103 LYS cc_start: 0.6788 (ttmm) cc_final: 0.6530 (mmtm) REVERT: R 166 MET cc_start: 0.7652 (ptt) cc_final: 0.7368 (ptp) REVERT: R 192 ASN cc_start: 0.7112 (m-40) cc_final: 0.6670 (t0) REVERT: R 286 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8109 (p) REVERT: R 288 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6591 (pt) outliers start: 26 outliers final: 18 residues processed: 119 average time/residue: 0.9334 time to fit residues: 118.3294 Evaluate side-chains 118 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN D 237 ASN ** R 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.180147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136574 restraints weight = 6983.626| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.18 r_work: 0.3522 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6810 Z= 0.203 Angle : 0.580 11.014 9312 Z= 0.298 Chirality : 0.040 0.134 1127 Planarity : 0.003 0.047 1155 Dihedral : 4.588 55.257 1125 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.63 % Allowed : 24.21 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.28), residues: 874 helix: 1.97 (0.26), residues: 386 sheet: -0.11 (0.38), residues: 173 loop : -0.92 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.008 0.001 HIS R 285 PHE 0.021 0.001 PHE R 165 TYR 0.012 0.001 TYR R 90 ARG 0.011 0.001 ARG C 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6286.22 seconds wall clock time: 107 minutes 32.57 seconds (6452.57 seconds total)