Starting phenix.real_space_refine on Fri Aug 22 23:01:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8id8_35359/08_2025/8id8_35359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8id8_35359/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8id8_35359/08_2025/8id8_35359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8id8_35359/08_2025/8id8_35359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8id8_35359/08_2025/8id8_35359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8id8_35359/08_2025/8id8_35359.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'PHE:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 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: {'ARG:plan': 6, 'ASP:plan': 2, 'HIS:plan': 2, 'GLU:plan': 4, 'TRP:plan': 2, 'GLN:plan1': 4, 'PHE:plan': 1} 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, 'ASP:plan': 1, 'ARG:plan': 2} 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: 1.51, per 1000 atoms: 0.17 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: 0.65 Conformation dependent library (CDL) restraints added in 420.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.21 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: 1.25 Time building geometry restraints manager: 0.86 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: 0.460 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.330 ------------------------------------------------------------------------------- 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 8808 Z= 0.227 Angle : 0.639 9.517 11962 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 : 8.98 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG B 129 TYR 0.015 0.002 TYR B 59 PHE 0.016 0.001 PHE B 234 TRP 0.010 0.001 TRP R 104 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8806) covalent geometry : angle 0.63791 (11958) SS BOND : bond 0.00652 ( 2) SS BOND : angle 2.21534 ( 4) hydrogen bonds : bond 0.14252 ( 419) hydrogen bonds : angle 6.19095 ( 1170) *********************** 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 : 0.196 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: 0.4301 time to fit residues: 70.5179 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 : 0.293 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4122 r_free = 0.4122 target = 0.182083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142351 restraints weight = 9118.047| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.06 r_work: 0.3361 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8808 Z= 0.142 Angle : 0.569 7.867 11962 Z= 0.300 Chirality : 0.043 0.148 1403 Planarity : 0.004 0.060 1500 Dihedral : 5.300 55.999 1231 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.33 % Allowed : 9.86 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.25), residues: 1115 helix: 1.48 (0.29), residues: 358 sheet: -0.74 (0.30), residues: 279 loop : -0.92 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 24 TYR 0.014 0.001 TYR S 191 PHE 0.020 0.001 PHE R 177 TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8806) covalent geometry : angle 0.56765 (11958) SS BOND : bond 0.00640 ( 2) SS BOND : angle 2.24171 ( 4) hydrogen bonds : bond 0.04259 ( 419) hydrogen bonds : angle 4.73515 ( 1170) *********************** 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 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.261 Fit side-chains REVERT: A 309 ASP cc_start: 0.7437 (m-30) cc_final: 0.7135 (m-30) REVERT: B 31 SER cc_start: 0.7948 (t) cc_final: 0.7672 (m) REVERT: R 47 LEU cc_start: 0.7034 (mt) cc_final: 0.6752 (mt) outliers start: 21 outliers final: 7 residues processed: 138 average time/residue: 0.4279 time to fit residues: 63.1407 Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** S 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.183908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144388 restraints weight = 9110.163| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.06 r_work: 0.3408 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8808 Z= 0.111 Angle : 0.515 7.977 11962 Z= 0.272 Chirality : 0.041 0.130 1403 Planarity : 0.004 0.056 1500 Dihedral : 4.994 52.665 1229 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 13.84 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.25), residues: 1115 helix: 1.80 (0.29), residues: 353 sheet: -0.55 (0.30), residues: 278 loop : -0.84 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.011 0.001 TYR S 191 PHE 0.013 0.001 PHE B 199 TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8806) covalent geometry : angle 0.51388 (11958) SS BOND : bond 0.00453 ( 2) SS BOND : angle 1.57913 ( 4) hydrogen bonds : bond 0.03704 ( 419) hydrogen bonds : angle 4.48700 ( 1170) *********************** 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 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7453 (m-30) cc_final: 0.7163 (m-30) REVERT: B 31 SER cc_start: 0.7878 (t) cc_final: 0.7633 (m) REVERT: B 298 ASP cc_start: 0.8454 (t0) cc_final: 0.8241 (t0) REVERT: R 214 LEU cc_start: 0.8432 (tp) cc_final: 0.8141 (tp) outliers start: 17 outliers final: 9 residues processed: 138 average time/residue: 0.4067 time to fit residues: 59.8865 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 92 ILE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.180879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140434 restraints weight = 9281.887| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.22 r_work: 0.3300 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8808 Z= 0.153 Angle : 0.542 6.772 11962 Z= 0.290 Chirality : 0.042 0.138 1403 Planarity : 0.004 0.062 1500 Dihedral : 5.088 47.902 1229 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.77 % Allowed : 13.62 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.25), residues: 1115 helix: 1.82 (0.28), residues: 353 sheet: -0.57 (0.30), residues: 280 loop : -0.86 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.012 0.001 TYR B 105 PHE 0.014 0.001 PHE B 199 TRP 0.009 0.001 TRP S 36 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8806) covalent geometry : angle 0.54121 (11958) SS BOND : bond 0.00511 ( 2) SS BOND : angle 1.69706 ( 4) hydrogen bonds : bond 0.04102 ( 419) hydrogen bonds : angle 4.47066 ( 1170) *********************** 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 154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7423 (m-30) cc_final: 0.7131 (m-30) REVERT: B 31 SER cc_start: 0.7851 (t) cc_final: 0.7550 (m) REVERT: B 43 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7833 (mp) REVERT: B 217 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7807 (ptm) REVERT: B 226 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: B 325 MET cc_start: 0.8317 (mmt) cc_final: 0.7841 (mmm) REVERT: R 214 LEU cc_start: 0.8445 (tp) cc_final: 0.8097 (tp) outliers start: 25 outliers final: 11 residues processed: 141 average time/residue: 0.4099 time to fit residues: 61.6497 Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 43 ILE Chi-restraints excluded: chain B residue 61 MET 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 86 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** 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** S 184 GLN 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 = 0.183632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.143965 restraints weight = 9091.408| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.09 r_work: 0.3338 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8808 Z= 0.110 Angle : 0.522 10.768 11962 Z= 0.272 Chirality : 0.041 0.157 1403 Planarity : 0.004 0.057 1500 Dihedral : 4.872 44.254 1229 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.99 % Allowed : 14.06 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.25), residues: 1115 helix: 1.86 (0.28), residues: 360 sheet: -0.43 (0.30), residues: 278 loop : -0.79 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.012 0.001 TYR S 191 PHE 0.014 0.001 PHE B 199 TRP 0.009 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8806) covalent geometry : angle 0.52142 (11958) SS BOND : bond 0.00394 ( 2) SS BOND : angle 1.22153 ( 4) hydrogen bonds : bond 0.03540 ( 419) hydrogen bonds : angle 4.32088 ( 1170) *********************** 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: 27 poor density : 130 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7368 (m-30) cc_final: 0.7070 (m-30) REVERT: B 23 LYS cc_start: 0.7194 (tppt) cc_final: 0.6921 (mmpt) REVERT: B 31 SER cc_start: 0.7730 (t) cc_final: 0.7467 (m) REVERT: B 226 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: B 262 MET cc_start: 0.7820 (mmt) cc_final: 0.7576 (mmt) REVERT: B 325 MET cc_start: 0.8305 (mmt) cc_final: 0.7809 (mmm) REVERT: R 68 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5964 (tmt-80) REVERT: R 214 LEU cc_start: 0.8473 (tp) cc_final: 0.8110 (tp) REVERT: Y 62 ARG cc_start: 0.5363 (ppt170) cc_final: 0.5143 (ppt170) outliers start: 27 outliers final: 13 residues processed: 145 average time/residue: 0.4164 time to fit residues: 64.6524 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 138 VAL 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 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 B 88 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.183322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143306 restraints weight = 9072.404| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.10 r_work: 0.3340 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8808 Z= 0.116 Angle : 0.523 8.805 11962 Z= 0.275 Chirality : 0.042 0.154 1403 Planarity : 0.004 0.055 1500 Dihedral : 4.864 45.514 1229 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.43 % Allowed : 14.51 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.25), residues: 1115 helix: 1.96 (0.28), residues: 360 sheet: -0.40 (0.30), residues: 279 loop : -0.69 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 27 TYR 0.011 0.001 TYR S 191 PHE 0.013 0.001 PHE B 199 TRP 0.008 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8806) covalent geometry : angle 0.52280 (11958) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.36408 ( 4) hydrogen bonds : bond 0.03574 ( 419) hydrogen bonds : angle 4.27841 ( 1170) *********************** 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 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 295 THR cc_start: 0.7791 (t) cc_final: 0.7508 (t) REVERT: A 309 ASP cc_start: 0.7412 (m-30) cc_final: 0.7141 (m-30) REVERT: B 31 SER cc_start: 0.7691 (t) cc_final: 0.7422 (m) REVERT: B 129 ARG cc_start: 0.7315 (mtp85) cc_final: 0.6872 (ttp80) REVERT: B 226 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: B 325 MET cc_start: 0.8322 (mmt) cc_final: 0.7860 (mmm) REVERT: R 68 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.6004 (tmt-80) REVERT: R 214 LEU cc_start: 0.8504 (tp) cc_final: 0.8120 (tp) REVERT: Y 62 ARG cc_start: 0.5391 (ppt170) cc_final: 0.5167 (ppt170) outliers start: 31 outliers final: 19 residues processed: 138 average time/residue: 0.3896 time to fit residues: 57.5225 Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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 47 LEU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 196 LEU 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 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** R 317 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 = 0.4138 r_free = 0.4138 target = 0.183827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143899 restraints weight = 9141.203| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.10 r_work: 0.3375 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8808 Z= 0.111 Angle : 0.507 7.788 11962 Z= 0.269 Chirality : 0.041 0.147 1403 Planarity : 0.004 0.054 1500 Dihedral : 4.787 46.518 1229 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.10 % Allowed : 15.28 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.25), residues: 1115 helix: 2.11 (0.28), residues: 359 sheet: -0.32 (0.30), residues: 277 loop : -0.69 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.011 0.001 TYR S 191 PHE 0.013 0.001 PHE B 199 TRP 0.008 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8806) covalent geometry : angle 0.50626 (11958) SS BOND : bond 0.00386 ( 2) SS BOND : angle 1.21194 ( 4) hydrogen bonds : bond 0.03492 ( 419) hydrogen bonds : angle 4.21563 ( 1170) *********************** 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 157 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7455 (m-30) cc_final: 0.7180 (m-30) REVERT: B 23 LYS cc_start: 0.7245 (tppt) cc_final: 0.6962 (mmpt) REVERT: B 31 SER cc_start: 0.7457 (t) cc_final: 0.7176 (m) REVERT: B 129 ARG cc_start: 0.7236 (mtp85) cc_final: 0.6934 (ttp80) REVERT: B 226 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: R 68 ARG cc_start: 0.6375 (OUTLIER) cc_final: 0.6111 (tmt-80) REVERT: R 214 LEU cc_start: 0.8514 (tp) cc_final: 0.8142 (tp) REVERT: S 214 THR cc_start: 0.8792 (t) cc_final: 0.8570 (m) REVERT: Y 62 ARG cc_start: 0.5488 (ppt170) cc_final: 0.5272 (ppt170) outliers start: 28 outliers final: 18 residues processed: 144 average time/residue: 0.3904 time to fit residues: 60.0712 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 : 0.266 ------------------------------------------------------------------------------- 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 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 81 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 173 LEU 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 140 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** ** R 317 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 = 0.4125 r_free = 0.4125 target = 0.182369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142256 restraints weight = 9023.272| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.13 r_work: 0.3371 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8808 Z= 0.129 Angle : 0.533 7.368 11962 Z= 0.282 Chirality : 0.042 0.162 1403 Planarity : 0.004 0.056 1500 Dihedral : 4.862 49.522 1229 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.10 % Allowed : 16.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1115 helix: 2.12 (0.28), residues: 360 sheet: -0.36 (0.30), residues: 279 loop : -0.68 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.009 0.001 TYR S 103 PHE 0.013 0.001 PHE B 199 TRP 0.007 0.001 TRP S 36 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8806) covalent geometry : angle 0.53259 (11958) SS BOND : bond 0.00440 ( 2) SS BOND : angle 1.25484 ( 4) hydrogen bonds : bond 0.03667 ( 419) hydrogen bonds : angle 4.24625 ( 1170) *********************** 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: 28 poor density : 119 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7465 (m-30) cc_final: 0.7190 (m-30) REVERT: B 129 ARG cc_start: 0.7288 (mtp85) cc_final: 0.6976 (ttp80) REVERT: B 226 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: R 68 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6362 (tmt-80) REVERT: R 214 LEU cc_start: 0.8521 (tp) cc_final: 0.8199 (tp) REVERT: S 214 THR cc_start: 0.8786 (t) cc_final: 0.8562 (m) REVERT: Y 62 ARG cc_start: 0.5383 (ppt170) cc_final: 0.5178 (ppt170) outliers start: 28 outliers final: 20 residues processed: 135 average time/residue: 0.5747 time to fit residues: 82.6312 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 47 LEU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 138 VAL 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 140 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 0.0020 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 100 optimal weight: 0.0170 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5428 ------------------------------------------------------------------------------- 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** ** R 317 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 = 0.4156 r_free = 0.4156 target = 0.185745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146056 restraints weight = 9038.996| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.08 r_work: 0.3402 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8808 Z= 0.101 Angle : 0.516 7.159 11962 Z= 0.270 Chirality : 0.042 0.196 1403 Planarity : 0.004 0.051 1500 Dihedral : 4.665 47.608 1229 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.21 % Allowed : 17.83 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.25), residues: 1115 helix: 2.25 (0.28), residues: 359 sheet: -0.28 (0.30), residues: 285 loop : -0.63 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.013 0.001 TYR S 191 PHE 0.013 0.001 PHE B 199 TRP 0.009 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8806) covalent geometry : angle 0.51578 (11958) SS BOND : bond 0.00334 ( 2) SS BOND : angle 0.93312 ( 4) hydrogen bonds : bond 0.03235 ( 419) hydrogen bonds : angle 4.14841 ( 1170) *********************** 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 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7458 (m-30) cc_final: 0.7181 (m-30) REVERT: B 23 LYS cc_start: 0.7284 (tppt) cc_final: 0.6984 (mmpt) REVERT: B 130 GLU cc_start: 0.7894 (mp0) cc_final: 0.7492 (mp0) REVERT: B 217 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7089 (ppp) REVERT: R 68 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6356 (tmt-80) REVERT: R 214 LEU cc_start: 0.8524 (tp) cc_final: 0.8166 (tp) REVERT: S 214 THR cc_start: 0.8782 (t) cc_final: 0.8566 (m) outliers start: 20 outliers final: 12 residues processed: 132 average time/residue: 0.5675 time to fit residues: 79.9700 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 68 ARG 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 142 THR Chi-restraints excluded: chain S residue 207 SER 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 55 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 15 optimal weight: 0.0030 chunk 102 optimal weight: 2.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- 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** ** R 317 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 = 0.4114 r_free = 0.4114 target = 0.181300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141100 restraints weight = 9084.596| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.14 r_work: 0.3385 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8808 Z= 0.156 Angle : 0.576 8.312 11962 Z= 0.306 Chirality : 0.044 0.201 1403 Planarity : 0.004 0.058 1500 Dihedral : 4.923 51.011 1229 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.99 % Allowed : 18.27 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1115 helix: 2.11 (0.28), residues: 360 sheet: -0.33 (0.30), residues: 284 loop : -0.63 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.012 0.001 TYR S 103 PHE 0.013 0.001 PHE B 199 TRP 0.009 0.001 TRP R 104 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8806) covalent geometry : angle 0.57560 (11958) SS BOND : bond 0.00499 ( 2) SS BOND : angle 1.37913 ( 4) hydrogen bonds : bond 0.03882 ( 419) hydrogen bonds : angle 4.28325 ( 1170) ********************** 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 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7532 (m-30) cc_final: 0.7256 (m-30) REVERT: B 23 LYS cc_start: 0.7366 (tppt) cc_final: 0.7052 (mmpt) REVERT: B 217 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7195 (ppp) REVERT: R 68 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6509 (tmt-80) REVERT: R 214 LEU cc_start: 0.8545 (tp) cc_final: 0.8210 (tp) REVERT: Y 21 MET cc_start: 0.6959 (ttt) cc_final: 0.6667 (ttt) outliers start: 18 outliers final: 13 residues processed: 134 average time/residue: 0.5803 time to fit residues: 83.0369 Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 R residue 68 ARG Chi-restraints excluded: chain R residue 81 LEU 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 142 THR Chi-restraints excluded: chain S residue 207 SER 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 41 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 62 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** ** R 317 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 = 0.4110 r_free = 0.4110 target = 0.181331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141679 restraints weight = 9145.575| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.21 r_work: 0.3352 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8808 Z= 0.131 Angle : 0.557 8.148 11962 Z= 0.295 Chirality : 0.043 0.204 1403 Planarity : 0.004 0.055 1500 Dihedral : 4.867 51.124 1229 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.99 % Allowed : 18.60 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.25), residues: 1115 helix: 2.14 (0.28), residues: 359 sheet: -0.33 (0.30), residues: 284 loop : -0.61 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.010 0.001 TYR S 191 PHE 0.014 0.001 PHE B 199 TRP 0.007 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8806) covalent geometry : angle 0.55698 (11958) SS BOND : bond 0.00436 ( 2) SS BOND : angle 1.18188 ( 4) hydrogen bonds : bond 0.03667 ( 419) hydrogen bonds : angle 4.26507 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.26 seconds wall clock time: 52 minutes 10.22 seconds (3130.22 seconds total)