Starting phenix.real_space_refine on Wed Feb 12 23:24:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8id8_35359/02_2025/8id8_35359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8id8_35359/02_2025/8id8_35359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8id8_35359/02_2025/8id8_35359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8id8_35359/02_2025/8id8_35359.map" model { file = "/net/cci-nas-00/data/ceres_data/8id8_35359/02_2025/8id8_35359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8id8_35359/02_2025/8id8_35359.cif" } resolution = 3.0 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= 0.011 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5518 2.51 5 N 1468 2.21 5 O 1588 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8635 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2554 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2170 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 102 Chain: "S" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Y" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 417 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'YN9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.36, per 1000 atoms: 0.62 Number of scatterers: 8635 At special positions: 0 Unit cell: (105.456, 125.736, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 1 9.00 O 1588 8.00 N 1468 7.00 C 5518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.03 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 35.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.463A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.740A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.640A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.617A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.213A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.665A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 37 through 68 Processing helix chain 'R' and resid 68 through 73 Processing helix chain 'R' and resid 78 through 101 removed outlier: 3.710A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 87 " --> pdb=" O CYS R 83 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 107 through 142 removed outlier: 3.885A pdb=" N CYS R 111 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS R 112 " --> pdb=" O PRO R 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 176 removed outlier: 3.768A pdb=" N ALA R 156 " --> pdb=" O ARG R 152 " (cutoff:3.500A) Proline residue: R 172 - end of helix removed outlier: 3.723A pdb=" N VAL R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 217 removed outlier: 3.820A pdb=" N SER R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 242 removed outlier: 3.661A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 277 removed outlier: 3.587A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE R 263 " --> pdb=" O ASP R 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 294 removed outlier: 3.617A pdb=" N ILE R 281 " --> pdb=" O TRP R 277 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 321 removed outlier: 3.502A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 8 through 23 Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.618A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.684A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.613A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.508A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.625A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.947A 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: 3.521A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.351A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AB4, first strand: chain 'S' and resid 195 through 196 removed outlier: 5.829A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 227 through 228 419 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2126 1.33 - 1.45: 1761 1.45 - 1.57: 4829 1.57 - 1.69: 4 1.69 - 1.82: 86 Bond restraints: 8806 Sorted by residual: bond pdb=" C1 YN9 R 401 " pdb=" C3 YN9 R 401 " ideal model delta sigma weight residual 1.481 1.595 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " ideal model delta sigma weight residual 1.501 1.606 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C1 YN9 R 401 " pdb=" C2 YN9 R 401 " ideal model delta sigma weight residual 1.400 1.486 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C9 YN9 R 401 " pdb=" O1 YN9 R 401 " ideal model delta sigma weight residual 1.353 1.432 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C5 YN9 R 401 " pdb=" C6 YN9 R 401 " ideal model delta sigma weight residual 1.503 1.580 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11708 1.90 - 3.81: 218 3.81 - 5.71: 23 5.71 - 7.61: 5 7.61 - 9.52: 4 Bond angle restraints: 11958 Sorted by residual: angle pdb=" N TYR S 229 " pdb=" CA TYR S 229 " pdb=" C TYR S 229 " ideal model delta sigma weight residual 109.40 116.29 -6.89 1.63e+00 3.76e-01 1.79e+01 angle pdb=" N LEU R 173 " pdb=" CA LEU R 173 " pdb=" C LEU R 173 " ideal model delta sigma weight residual 111.82 116.17 -4.35 1.16e+00 7.43e-01 1.41e+01 angle pdb=" N ASP R 30 " pdb=" CA ASP R 30 " pdb=" C ASP R 30 " ideal model delta sigma weight residual 109.24 115.20 -5.96 1.67e+00 3.59e-01 1.27e+01 angle pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " pdb=" O1 YN9 R 401 " ideal model delta sigma weight residual 107.97 117.49 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N GLU Y 58 " pdb=" CA GLU Y 58 " pdb=" C GLU Y 58 " ideal model delta sigma weight residual 111.36 114.57 -3.21 1.09e+00 8.42e-01 8.69e+00 ... (remaining 11953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.31: 4811 20.31 - 40.62: 337 40.62 - 60.93: 41 60.93 - 81.24: 6 81.24 - 101.55: 1 Dihedral angle restraints: 5196 sinusoidal: 1904 harmonic: 3292 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 54.40 38.60 1 1.00e+01 1.00e-02 2.10e+01 dihedral pdb=" CA GLN S 143 " pdb=" C GLN S 143 " pdb=" N ALA S 144 " pdb=" CA ALA S 144 " ideal model delta harmonic sigma weight residual 180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 959 0.040 - 0.080: 323 0.080 - 0.119: 103 0.119 - 0.159: 17 0.159 - 0.199: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA THR Y 52 " pdb=" N THR Y 52 " pdb=" C THR Y 52 " pdb=" CB THR Y 52 " both_signs ideal model delta sigma weight residual False 2.53 2.72 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1400 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 282 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO S 107 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 54 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C VAL Y 54 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL Y 54 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO Y 55 " 0.012 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 3 2.09 - 2.80: 2119 2.80 - 3.50: 11287 3.50 - 4.20: 19674 4.20 - 4.90: 36008 Nonbonded interactions: 69091 Sorted by model distance: nonbonded pdb=" OH TYR A 230 " pdb=" CE1 PHE A 274 " model vdw 1.393 3.340 nonbonded pdb=" OD1 ASP A 341 " pdb=" NH1 ARG R 238 " model vdw 1.998 3.120 nonbonded pdb=" OH TYR A 230 " pdb=" CD1 PHE A 274 " model vdw 2.063 3.340 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.104 3.040 nonbonded pdb=" OH TYR R 165 " pdb=" OD1 ASN R 215 " model vdw 2.155 3.040 ... (remaining 69086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.340 Find NCS groups from input model: 0.120 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.114 8806 Z= 0.293 Angle : 0.638 9.517 11958 Z= 0.358 Chirality : 0.044 0.199 1403 Planarity : 0.004 0.067 1500 Dihedral : 13.406 101.546 3058 Min Nonbonded Distance : 1.393 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.33 % Allowed : 0.78 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.43 (0.25), residues: 1115 helix: 1.13 (0.29), residues: 353 sheet: -0.82 (0.29), residues: 284 loop : -0.94 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 104 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.001 PHE B 234 TYR 0.015 0.002 TYR B 59 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8191 (mttm) cc_final: 0.7982 (mttp) REVERT: A 208 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7764 (ttm110) REVERT: A 309 ASP cc_start: 0.7671 (m-30) cc_final: 0.7431 (m-30) REVERT: B 325 MET cc_start: 0.7529 (mmt) cc_final: 0.7132 (mmm) REVERT: R 47 LEU cc_start: 0.7519 (mt) cc_final: 0.7213 (mt) outliers start: 3 outliers final: 1 residues processed: 154 average time/residue: 1.2602 time to fit residues: 207.0290 Evaluate side-chains 120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 204 GLN B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.181468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141691 restraints weight = 9069.803| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.06 r_work: 0.3369 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8806 Z= 0.227 Angle : 0.573 7.931 11958 Z= 0.302 Chirality : 0.043 0.150 1403 Planarity : 0.005 0.061 1500 Dihedral : 5.333 56.420 1231 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.33 % Allowed : 9.97 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.21 (0.25), residues: 1115 helix: 1.46 (0.29), residues: 358 sheet: -0.74 (0.30), residues: 279 loop : -0.93 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.001 PHE R 177 TYR 0.014 0.001 TYR S 191 ARG 0.005 0.000 ARG R 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.836 Fit side-chains REVERT: A 309 ASP cc_start: 0.7448 (m-30) cc_final: 0.7145 (m-30) REVERT: B 31 SER cc_start: 0.7968 (t) cc_final: 0.7672 (m) REVERT: R 47 LEU cc_start: 0.7037 (mt) cc_final: 0.6751 (mt) REVERT: S 193 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7800 (ttp) outliers start: 21 outliers final: 8 residues processed: 136 average time/residue: 1.1976 time to fit residues: 174.2313 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 193 MET Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.171543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130925 restraints weight = 9462.909| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.63 r_work: 0.3260 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8806 Z= 0.257 Angle : 0.569 7.190 11958 Z= 0.303 Chirality : 0.043 0.140 1403 Planarity : 0.004 0.065 1500 Dihedral : 5.290 50.747 1229 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.77 % Allowed : 13.07 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.14 (0.25), residues: 1115 helix: 1.56 (0.28), residues: 355 sheet: -0.68 (0.29), residues: 280 loop : -0.92 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS A 213 PHE 0.015 0.002 PHE B 199 TYR 0.015 0.002 TYR B 105 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7451 (m-30) cc_final: 0.7160 (m-30) REVERT: B 31 SER cc_start: 0.7925 (t) cc_final: 0.7648 (m) REVERT: B 325 MET cc_start: 0.8346 (mmt) cc_final: 0.7851 (mmm) REVERT: R 68 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.5693 (ttp-170) REVERT: R 214 LEU cc_start: 0.8465 (tp) cc_final: 0.8168 (tp) outliers start: 25 outliers final: 12 residues processed: 140 average time/residue: 1.1612 time to fit residues: 174.0359 Evaluate side-chains 132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.168026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126844 restraints weight = 9444.881| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.54 r_work: 0.3195 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8806 Z= 0.311 Angle : 0.593 7.393 11958 Z= 0.317 Chirality : 0.044 0.151 1403 Planarity : 0.005 0.071 1500 Dihedral : 5.428 51.653 1229 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.65 % Allowed : 14.62 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.16 (0.25), residues: 1115 helix: 1.50 (0.28), residues: 355 sheet: -0.60 (0.29), residues: 289 loop : -0.96 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 63 HIS 0.006 0.001 HIS A 213 PHE 0.016 0.002 PHE B 199 TYR 0.014 0.002 TYR B 59 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7395 (m-30) cc_final: 0.7100 (m-30) REVERT: B 23 LYS cc_start: 0.7310 (tppt) cc_final: 0.7076 (mmpt) REVERT: B 31 SER cc_start: 0.7850 (t) cc_final: 0.7545 (m) REVERT: B 43 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7680 (mp) REVERT: B 118 ASP cc_start: 0.8044 (t0) cc_final: 0.7840 (t0) REVERT: B 217 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7841 (ptm) REVERT: B 226 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: B 325 MET cc_start: 0.8307 (mmt) cc_final: 0.7824 (mmm) REVERT: R 68 ARG cc_start: 0.6066 (OUTLIER) cc_final: 0.5782 (tmt-80) REVERT: R 77 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.7024 (tp) REVERT: R 214 LEU cc_start: 0.8403 (tp) cc_final: 0.8052 (tp) REVERT: S 214 THR cc_start: 0.8752 (t) cc_final: 0.8526 (m) outliers start: 33 outliers final: 14 residues processed: 147 average time/residue: 1.0960 time to fit residues: 172.8745 Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 88 ASN ** R 58 ASN ** 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 = 0.3919 r_free = 0.3919 target = 0.167927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124892 restraints weight = 9381.759| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.51 r_work: 0.3175 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8806 Z= 0.255 Angle : 0.573 9.374 11958 Z= 0.305 Chirality : 0.043 0.180 1403 Planarity : 0.004 0.067 1500 Dihedral : 5.338 53.087 1229 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.10 % Allowed : 15.28 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.13 (0.25), residues: 1115 helix: 1.46 (0.28), residues: 361 sheet: -0.57 (0.29), residues: 288 loop : -0.95 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.006 0.001 HIS S 35 PHE 0.016 0.001 PHE B 199 TYR 0.011 0.001 TYR S 103 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7373 (m-30) cc_final: 0.7076 (m-30) REVERT: A 345 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7367 (mtmt) REVERT: B 118 ASP cc_start: 0.8282 (t0) cc_final: 0.7987 (t0) REVERT: B 226 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: B 300 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 325 MET cc_start: 0.8297 (mmt) cc_final: 0.7795 (mmm) REVERT: R 68 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5764 (tmt-80) REVERT: R 77 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.7016 (tp) REVERT: R 214 LEU cc_start: 0.8449 (tp) cc_final: 0.8100 (tp) REVERT: S 214 THR cc_start: 0.8744 (t) cc_final: 0.8517 (m) outliers start: 37 outliers final: 19 residues processed: 143 average time/residue: 1.1211 time to fit residues: 171.9429 Evaluate side-chains 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.181741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141962 restraints weight = 9013.717| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.09 r_work: 0.3351 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8806 Z= 0.177 Angle : 0.529 7.099 11958 Z= 0.281 Chirality : 0.042 0.183 1403 Planarity : 0.004 0.060 1500 Dihedral : 5.110 52.200 1229 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.99 % Allowed : 15.84 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.06 (0.25), residues: 1115 helix: 1.68 (0.28), residues: 360 sheet: -0.49 (0.30), residues: 278 loop : -0.86 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.012 0.001 TYR S 191 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 295 THR cc_start: 0.7832 (t) cc_final: 0.7548 (t) REVERT: A 309 ASP cc_start: 0.7451 (m-30) cc_final: 0.7147 (m-30) REVERT: A 345 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7416 (mtmt) REVERT: B 23 LYS cc_start: 0.7279 (tppt) cc_final: 0.7000 (mmpt) REVERT: B 118 ASP cc_start: 0.8353 (t0) cc_final: 0.8007 (t0) REVERT: B 226 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: B 325 MET cc_start: 0.8336 (mmt) cc_final: 0.7861 (mmm) REVERT: R 77 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6969 (tp) REVERT: R 214 LEU cc_start: 0.8522 (tp) cc_final: 0.8156 (tp) REVERT: S 214 THR cc_start: 0.8755 (t) cc_final: 0.8528 (m) REVERT: Y 62 ARG cc_start: 0.5360 (ppt170) cc_final: 0.5144 (ppt170) outliers start: 27 outliers final: 15 residues processed: 144 average time/residue: 1.1363 time to fit residues: 175.3173 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 18 optimal weight: 0.0470 chunk 90 optimal weight: 0.0570 chunk 56 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.180323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140700 restraints weight = 9093.008| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.19 r_work: 0.3349 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8806 Z= 0.175 Angle : 0.531 9.185 11958 Z= 0.280 Chirality : 0.042 0.193 1403 Planarity : 0.004 0.057 1500 Dihedral : 4.989 51.793 1229 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.99 % Allowed : 16.83 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.21 (0.25), residues: 1115 helix: 1.86 (0.28), residues: 360 sheet: -0.44 (0.30), residues: 278 loop : -0.79 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR S 191 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7476 (m-30) cc_final: 0.7182 (m-30) REVERT: B 118 ASP cc_start: 0.8418 (t0) cc_final: 0.8070 (t0) REVERT: B 129 ARG cc_start: 0.7389 (mtp85) cc_final: 0.6988 (ttp80) REVERT: B 226 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: B 325 MET cc_start: 0.8364 (mmt) cc_final: 0.7910 (mmm) REVERT: R 77 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6958 (tp) REVERT: R 214 LEU cc_start: 0.8490 (tp) cc_final: 0.8106 (tp) REVERT: S 214 THR cc_start: 0.8758 (t) cc_final: 0.8521 (m) REVERT: Y 21 MET cc_start: 0.6975 (tmt) cc_final: 0.6201 (ttp) outliers start: 27 outliers final: 18 residues processed: 141 average time/residue: 1.2055 time to fit residues: 182.5265 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 232 GLN Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.170303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.129805 restraints weight = 9516.085| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.57 r_work: 0.3206 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8806 Z= 0.328 Angle : 0.615 8.986 11958 Z= 0.327 Chirality : 0.045 0.181 1403 Planarity : 0.004 0.067 1500 Dihedral : 5.372 56.754 1229 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.43 % Allowed : 17.05 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.00 (0.25), residues: 1115 helix: 1.62 (0.28), residues: 360 sheet: -0.52 (0.29), residues: 294 loop : -0.88 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 36 HIS 0.007 0.002 HIS S 35 PHE 0.014 0.002 PHE B 199 TYR 0.013 0.002 TYR S 103 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7387 (mt0) cc_final: 0.7181 (tt0) REVERT: A 309 ASP cc_start: 0.7517 (m-30) cc_final: 0.7231 (m-30) REVERT: A 345 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7529 (mtmt) REVERT: B 23 LYS cc_start: 0.7394 (tppt) cc_final: 0.7090 (mmpt) REVERT: B 118 ASP cc_start: 0.8521 (t0) cc_final: 0.8172 (t0) REVERT: B 217 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.6909 (ppp) REVERT: B 226 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: R 77 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7079 (tp) REVERT: R 214 LEU cc_start: 0.8476 (tp) cc_final: 0.8193 (tp) REVERT: S 22 CYS cc_start: 0.8034 (t) cc_final: 0.7599 (p) REVERT: S 214 THR cc_start: 0.8748 (t) cc_final: 0.8508 (m) REVERT: Y 21 MET cc_start: 0.6968 (tmt) cc_final: 0.6064 (ttp) outliers start: 31 outliers final: 21 residues processed: 137 average time/residue: 1.1803 time to fit residues: 172.9508 Evaluate side-chains 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 232 GLN Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.180708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141094 restraints weight = 9183.710| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.22 r_work: 0.3404 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8806 Z= 0.170 Angle : 0.534 8.432 11958 Z= 0.281 Chirality : 0.042 0.174 1403 Planarity : 0.004 0.058 1500 Dihedral : 5.025 54.729 1229 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.21 % Allowed : 18.05 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.24 (0.25), residues: 1115 helix: 1.92 (0.28), residues: 360 sheet: -0.47 (0.30), residues: 277 loop : -0.77 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR S 191 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7559 (m-30) cc_final: 0.7266 (m-30) REVERT: A 345 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7543 (mtmt) REVERT: B 23 LYS cc_start: 0.7427 (tppt) cc_final: 0.7128 (mmpt) REVERT: B 118 ASP cc_start: 0.8456 (t0) cc_final: 0.8091 (t0) REVERT: B 129 ARG cc_start: 0.7400 (mtp85) cc_final: 0.7069 (ttp80) REVERT: B 217 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7356 (ppp) REVERT: B 226 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: R 77 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.7024 (tp) REVERT: R 214 LEU cc_start: 0.8502 (tp) cc_final: 0.8152 (tp) REVERT: S 214 THR cc_start: 0.8755 (t) cc_final: 0.8520 (m) REVERT: Y 21 MET cc_start: 0.7018 (tmt) cc_final: 0.6190 (ttp) outliers start: 29 outliers final: 18 residues processed: 134 average time/residue: 1.1589 time to fit residues: 166.1067 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 232 GLN Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 0.0050 chunk 6 optimal weight: 7.9990 chunk 81 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 32 optimal weight: 0.0060 chunk 24 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 101 optimal weight: 0.0020 overall best weight: 0.1136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 32 GLN R 58 ASN ** R 80 ASN ** 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 = 0.4177 r_free = 0.4177 target = 0.188182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.149057 restraints weight = 9048.248| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.99 r_work: 0.3510 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8806 Z= 0.130 Angle : 0.502 8.174 11958 Z= 0.263 Chirality : 0.041 0.171 1403 Planarity : 0.004 0.050 1500 Dihedral : 4.656 50.236 1229 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.44 % Allowed : 20.16 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.53 (0.25), residues: 1115 helix: 2.30 (0.28), residues: 359 sheet: -0.39 (0.30), residues: 283 loop : -0.66 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.002 0.000 HIS S 35 PHE 0.013 0.001 PHE R 88 TYR 0.013 0.001 TYR S 191 ARG 0.006 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 295 THR cc_start: 0.7661 (t) cc_final: 0.7431 (t) REVERT: A 309 ASP cc_start: 0.7553 (m-30) cc_final: 0.7270 (m-30) REVERT: A 345 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7146 (mttp) REVERT: B 118 ASP cc_start: 0.8370 (t0) cc_final: 0.7945 (t0) REVERT: B 130 GLU cc_start: 0.7910 (mp0) cc_final: 0.7378 (mp0) REVERT: B 217 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7238 (ppp) REVERT: B 325 MET cc_start: 0.8324 (mmt) cc_final: 0.7928 (mmm) REVERT: R 214 LEU cc_start: 0.8403 (tp) cc_final: 0.8011 (tp) REVERT: S 80 PHE cc_start: 0.7906 (m-80) cc_final: 0.7682 (m-80) REVERT: S 214 THR cc_start: 0.8753 (t) cc_final: 0.8533 (m) REVERT: Y 21 MET cc_start: 0.6991 (tmt) cc_final: 0.6391 (ttp) outliers start: 13 outliers final: 8 residues processed: 139 average time/residue: 1.0991 time to fit residues: 164.1023 Evaluate side-chains 126 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 78 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.186546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147333 restraints weight = 9065.352| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.15 r_work: 0.3471 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8806 Z= 0.155 Angle : 0.539 12.747 11958 Z= 0.277 Chirality : 0.042 0.168 1403 Planarity : 0.004 0.050 1500 Dihedral : 4.630 50.383 1229 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.66 % Allowed : 21.26 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.63 (0.25), residues: 1115 helix: 2.39 (0.28), residues: 359 sheet: -0.35 (0.30), residues: 283 loop : -0.60 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR S 191 ARG 0.007 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7371.52 seconds wall clock time: 130 minutes 32.47 seconds (7832.47 seconds total)