Starting phenix.real_space_refine on Fri Oct 23 05:17:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x74_66632/10_2026/9x74_66632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x74_66632/10_2026/9x74_66632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x74_66632/10_2026/9x74_66632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x74_66632/10_2026/9x74_66632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x74_66632/10_2026/9x74_66632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x74_66632/10_2026/9x74_66632.map" } resolution = 3.15 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5410 2.51 5 N 1464 2.21 5 O 1541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8468 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2473 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1710 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2208 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1727 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 2.20, per 1000 atoms: 0.26 Number of scatterers: 8468 At special positions: 0 Unit cell: (106.72, 110.2, 143.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1541 8.00 N 1464 7.00 C 5410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 130 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 543.2 milliseconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 37.3% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.725A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.630A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.818A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 4.158A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.041A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 removed outlier: 3.738A pdb=" N ARG A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 87 removed outlier: 4.040A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix removed outlier: 3.610A pdb=" N PHE R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 117 removed outlier: 3.748A pdb=" N ASN R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 125 removed outlier: 3.693A pdb=" N GLU R 121 " --> pdb=" O ASN R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 161 removed outlier: 4.070A pdb=" N SER R 134 " --> pdb=" O CYS R 130 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN R 138 " --> pdb=" O SER R 134 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL R 145 " --> pdb=" O MET R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 191 Processing helix chain 'R' and resid 214 through 223 removed outlier: 3.916A pdb=" N GLU R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE R 223 " --> pdb=" O VAL R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 249 removed outlier: 3.720A pdb=" N ALA R 228 " --> pdb=" O ILE R 224 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG R 246 " --> pdb=" O VAL R 242 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS R 247 " --> pdb=" O ARG R 243 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY R 249 " --> pdb=" O HIS R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 253 No H-bonds generated for 'chain 'R' and resid 251 through 253' Processing helix chain 'R' and resid 254 through 261 removed outlier: 3.602A pdb=" N LEU R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 285 Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.845A pdb=" N ASN R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 339 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.512A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 179 through 181 No H-bonds generated for 'chain 'S' and resid 179 through 181' Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.445A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.757A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.395A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.618A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.837A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.416A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.648A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 73 through 76 removed outlier: 3.833A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.878A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.716A pdb=" N ARG S 148 " --> pdb=" O THR S 129 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.865A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1158 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: 1.00 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2756 1.34 - 1.46: 2097 1.46 - 1.58: 3724 1.58 - 1.70: 0 1.70 - 1.81: 75 Bond restraints: 8652 Sorted by residual: bond pdb=" N GLN G 11 " pdb=" CA GLN G 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N LEU B 4 " pdb=" CA LEU B 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N SER R 50 " pdb=" CA SER R 50 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N VAL A 5 " pdb=" CA VAL A 5 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N VAL S 2 " pdb=" CA VAL S 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 8647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 11294 1.19 - 2.37: 373 2.37 - 3.56: 75 3.56 - 4.74: 14 4.74 - 5.93: 2 Bond angle restraints: 11758 Sorted by residual: angle pdb=" N VAL R 264 " pdb=" CA VAL R 264 " pdb=" C VAL R 264 " ideal model delta sigma weight residual 112.96 108.48 4.48 1.00e+00 1.00e+00 2.00e+01 angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 111.13 2.07 9.60e-01 1.09e+00 4.63e+00 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.01 110.48 2.53 1.20e+00 6.94e-01 4.44e+00 angle pdb=" N PRO R 252 " pdb=" CA PRO R 252 " pdb=" C PRO R 252 " ideal model delta sigma weight residual 114.20 111.70 2.50 1.20e+00 6.94e-01 4.35e+00 angle pdb=" N VAL R 214 " pdb=" CA VAL R 214 " pdb=" C VAL R 214 " ideal model delta sigma weight residual 111.91 110.08 1.83 8.90e-01 1.26e+00 4.21e+00 ... (remaining 11753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.09: 4315 15.09 - 30.17: 540 30.17 - 45.26: 187 45.26 - 60.35: 32 60.35 - 75.43: 11 Dihedral angle restraints: 5085 sinusoidal: 1868 harmonic: 3217 Sorted by residual: dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.78 39.22 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 130.76 -37.76 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" CA GLU A 71 " pdb=" C GLU A 71 " pdb=" N THR A 72 " pdb=" CA THR A 72 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 848 0.029 - 0.059: 325 0.059 - 0.088: 93 0.088 - 0.117: 67 0.117 - 0.146: 19 Chirality restraints: 1352 Sorted by residual: 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 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1349 not shown) Planarity restraints: 1493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 320 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO R 321 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 321 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 321 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 323 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" C ILE R 323 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE R 323 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR R 324 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 93 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO R 94 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 94 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 94 " 0.018 5.00e-02 4.00e+02 ... (remaining 1490 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 242 2.68 - 3.24: 8541 3.24 - 3.79: 13064 3.79 - 4.35: 17677 4.35 - 4.90: 30148 Nonbonded interactions: 69672 Sorted by model distance: nonbonded pdb=" O ILE S 145 " pdb=" OG1 THR S 201 " model vdw 2.128 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.135 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.153 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG1 THR S 57 " model vdw 2.190 3.040 nonbonded pdb=" O ARG A 135 " pdb=" ND1 HIS A 209 " model vdw 2.248 3.120 ... (remaining 69667 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 : 0.003 0.036 8655 Z= 0.132 Angle : 0.528 5.926 11764 Z= 0.293 Chirality : 0.040 0.146 1352 Planarity : 0.004 0.039 1493 Dihedral : 15.533 75.435 2996 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.23 % Allowed : 19.98 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.55 (0.26), residues: 1088 helix: 0.95 (0.28), residues: 373 sheet: -0.90 (0.30), residues: 279 loop : -1.06 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 148 TYR 0.013 0.001 TYR R 324 PHE 0.013 0.001 PHE A 215 TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8652) covalent geometry : angle 0.52774 / 0.29 (11758) SS BOND : bond 0.00278 / 0.14 ( 3) SS BOND : angle 0.60850 / 0.31 ( 6) hydrogen bonds : bond 0.13172 / 9.48 ( 416) hydrogen bonds : angle 6.13941 / 4.28 ( 1158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 49 ARG cc_start: 0.7419 (mpt180) cc_final: 0.7175 (mpp-170) REVERT: B 63 TRP cc_start: 0.7535 (m100) cc_final: 0.7312 (m100) REVERT: B 127 LYS cc_start: 0.7523 (tptp) cc_final: 0.6496 (mttt) REVERT: B 129 ARG cc_start: 0.5140 (mmp-170) cc_final: 0.4927 (mmm160) REVERT: B 188 MET cc_start: 0.5925 (mtp) cc_final: 0.5515 (mmt) REVERT: A 35 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7081 (mtm180) REVERT: A 46 LYS cc_start: 0.6071 (ttpt) cc_final: 0.5818 (ttpp) REVERT: A 124 ASP cc_start: 0.4518 (t0) cc_final: 0.4003 (t0) REVERT: A 196 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7336 (mm-30) REVERT: A 238 MET cc_start: 0.7515 (tmm) cc_final: 0.7141 (tmm) REVERT: R 60 PHE cc_start: 0.7593 (t80) cc_final: 0.7389 (t80) REVERT: R 168 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.6101 (m-80) REVERT: S 128 MET cc_start: 0.5445 (ptp) cc_final: 0.5023 (ptp) outliers start: 2 outliers final: 1 residues processed: 177 average time/residue: 0.0987 time to fit residues: 23.6339 Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 168 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS A 75 GLN A 214 HIS ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 HIS R 285 GLN R 316 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.229594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.190341 restraints weight = 10365.316| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.25 r_work: 0.4170 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8655 Z= 0.147 Angle : 0.620 7.000 11764 Z= 0.322 Chirality : 0.044 0.188 1352 Planarity : 0.004 0.055 1493 Dihedral : 5.085 50.474 1203 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.54 % Allowed : 19.06 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.23 (0.26), residues: 1088 helix: 1.08 (0.27), residues: 380 sheet: -0.43 (0.32), residues: 259 loop : -0.99 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 117 TYR 0.017 0.002 TYR R 324 PHE 0.014 0.002 PHE R 227 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8652) covalent geometry : angle 0.61997 / 0.32 (11758) SS BOND : bond 0.00455 / 0.23 ( 3) SS BOND : angle 0.92456 / 0.52 ( 6) hydrogen bonds : bond 0.03902 / 2.73 ( 416) hydrogen bonds : angle 4.93450 / 3.43 ( 1158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6664 (mpp-170) REVERT: B 128 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7554 (t) REVERT: B 188 MET cc_start: 0.5992 (mtp) cc_final: 0.5768 (mmt) REVERT: B 220 GLN cc_start: 0.5794 (mp10) cc_final: 0.5581 (mp10) REVERT: A 35 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7518 (mtm180) REVERT: A 124 ASP cc_start: 0.4420 (t0) cc_final: 0.4118 (t0) REVERT: A 196 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7100 (mm-30) REVERT: R 60 PHE cc_start: 0.7631 (t80) cc_final: 0.7339 (t80) REVERT: R 164 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7252 (mtm180) REVERT: S 128 MET cc_start: 0.4820 (ptp) cc_final: 0.4531 (ptp) outliers start: 31 outliers final: 17 residues processed: 162 average time/residue: 0.0877 time to fit residues: 19.7763 Evaluate side-chains 137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 154 ASP Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 109 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [42, 37, 81, 55, 103, 82, 24, 80, 2, 101, 97] chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 81 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN R 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.237128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.199356 restraints weight = 10169.639| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.04 r_work: 0.4267 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8655 Z= 0.151 Angle : 0.595 6.436 11764 Z= 0.309 Chirality : 0.043 0.200 1352 Planarity : 0.004 0.055 1493 Dihedral : 4.744 49.614 1201 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.57 % Allowed : 19.63 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.16 (0.26), residues: 1088 helix: 1.12 (0.27), residues: 380 sheet: -0.30 (0.32), residues: 269 loop : -0.99 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.018 0.002 TYR R 324 PHE 0.014 0.002 PHE R 227 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS R 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8652) covalent geometry : angle 0.59460 / 0.31 (11758) SS BOND : bond 0.00450 / 0.23 ( 3) SS BOND : angle 0.81828 / 0.43 ( 6) hydrogen bonds : bond 0.03808 / 2.68 ( 416) hydrogen bonds : angle 4.81233 / 3.33 ( 1158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: B 188 MET cc_start: 0.6138 (mtp) cc_final: 0.5900 (mmt) REVERT: B 220 GLN cc_start: 0.5928 (mp10) cc_final: 0.5710 (mp10) REVERT: B 262 MET cc_start: 0.5605 (mmm) cc_final: 0.5275 (mmm) REVERT: A 35 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7497 (mtm180) REVERT: A 124 ASP cc_start: 0.4515 (t0) cc_final: 0.3899 (t70) REVERT: A 146 GLN cc_start: 0.6098 (tt0) cc_final: 0.5884 (tt0) REVERT: R 97 TYR cc_start: 0.6887 (m-10) cc_final: 0.6652 (m-10) REVERT: R 164 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7281 (mtm180) REVERT: R 215 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7398 (mt0) outliers start: 40 outliers final: 24 residues processed: 165 average time/residue: 0.0924 time to fit residues: 21.1289 Evaluate side-chains 143 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 140 ASN Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 329 GLU Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [34, 5, 70, 6, 46, 71, 24, 87, 107, 93, 57] chunk 34 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 57 optimal weight: 0.0040 overall best weight: 0.7374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.238686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.203605 restraints weight = 10410.810| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 2.14 r_work: 0.4241 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8655 Z= 0.126 Angle : 0.577 6.690 11764 Z= 0.300 Chirality : 0.042 0.238 1352 Planarity : 0.004 0.058 1493 Dihedral : 4.616 48.620 1201 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.45 % Allowed : 20.09 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.04 (0.26), residues: 1088 helix: 1.18 (0.27), residues: 379 sheet: -0.20 (0.32), residues: 269 loop : -0.92 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.018 0.001 TYR R 324 PHE 0.018 0.002 PHE R 60 TRP 0.021 0.001 TRP A 129 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8652) covalent geometry : angle 0.57712 / 0.30 (11758) SS BOND : bond 0.00438 / 0.22 ( 3) SS BOND : angle 0.72270 / 0.38 ( 6) hydrogen bonds : bond 0.03493 / 2.45 ( 416) hydrogen bonds : angle 4.66397 / 3.22 ( 1158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: B 49 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6451 (mpt180) REVERT: B 75 GLN cc_start: 0.3862 (OUTLIER) cc_final: 0.3220 (tm-30) REVERT: B 220 GLN cc_start: 0.5894 (mp10) cc_final: 0.5675 (mp10) REVERT: B 262 MET cc_start: 0.5603 (mmm) cc_final: 0.5353 (mmm) REVERT: A 18 MET cc_start: 0.6527 (ptp) cc_final: 0.6222 (ptm) REVERT: A 35 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7472 (mtm180) REVERT: A 124 ASP cc_start: 0.4453 (t0) cc_final: 0.4230 (t0) REVERT: A 232 LYS cc_start: 0.7761 (ttmt) cc_final: 0.7352 (ttpp) REVERT: R 97 TYR cc_start: 0.6890 (m-10) cc_final: 0.6684 (m-10) REVERT: R 215 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7250 (mt0) REVERT: R 275 GLU cc_start: 0.7141 (tt0) cc_final: 0.6884 (tt0) outliers start: 39 outliers final: 23 residues processed: 162 average time/residue: 0.0899 time to fit residues: 20.2676 Evaluate side-chains 147 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 329 GLU Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [40, 77, 69, 67, 46, 84, 39, 26, 92, 18, 58] chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN S 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.236188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.201321 restraints weight = 10302.524| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 2.11 r_work: 0.4248 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8655 Z= 0.166 Angle : 0.600 6.750 11764 Z= 0.312 Chirality : 0.044 0.260 1352 Planarity : 0.004 0.056 1493 Dihedral : 4.449 19.038 1199 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.37 % Allowed : 20.55 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.07 (0.26), residues: 1088 helix: 1.11 (0.27), residues: 381 sheet: -0.18 (0.32), residues: 274 loop : -0.92 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.016 0.002 TYR R 324 PHE 0.019 0.002 PHE A 215 TRP 0.018 0.002 TRP A 129 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 8652) covalent geometry : angle 0.59963 / 0.31 (11758) SS BOND : bond 0.00796 / 0.41 ( 3) SS BOND : angle 0.72617 / 0.37 ( 6) hydrogen bonds : bond 0.03849 / 2.70 ( 416) hydrogen bonds : angle 4.77228 / 3.31 ( 1158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 TRP cc_start: 0.7685 (m100) cc_final: 0.7370 (m100) REVERT: B 75 GLN cc_start: 0.4119 (OUTLIER) cc_final: 0.3456 (tm-30) REVERT: B 222 PHE cc_start: 0.4053 (OUTLIER) cc_final: 0.2553 (m-80) REVERT: B 325 MET cc_start: 0.5771 (tpp) cc_final: 0.4327 (ptt) REVERT: A 232 LYS cc_start: 0.7670 (ttmt) cc_final: 0.7285 (ttpp) REVERT: R 275 GLU cc_start: 0.7556 (tt0) cc_final: 0.7341 (tt0) outliers start: 47 outliers final: 28 residues processed: 163 average time/residue: 0.0829 time to fit residues: 18.7935 Evaluate side-chains 148 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 154 ASP Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 240 VAL Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [106, 96, 37, 10, 28, 60, 39, 67, 83, 95, 72] chunk 106 optimal weight: 10.0000 chunk 96 optimal weight: 0.2980 chunk 37 optimal weight: 0.0000 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.239847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.207070 restraints weight = 10185.188| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 2.05 r_work: 0.4309 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8655 Z= 0.113 Angle : 0.556 6.681 11764 Z= 0.290 Chirality : 0.042 0.216 1352 Planarity : 0.004 0.057 1493 Dihedral : 4.203 17.568 1199 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.65 % Allowed : 22.49 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 0.08 (0.26), residues: 1088 helix: 1.29 (0.27), residues: 380 sheet: -0.13 (0.32), residues: 269 loop : -0.85 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.018 0.001 TYR R 324 PHE 0.023 0.001 PHE R 60 TRP 0.025 0.001 TRP A 129 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8652) covalent geometry : angle 0.55638 / 0.29 (11758) SS BOND : bond 0.00475 / 0.24 ( 3) SS BOND : angle 0.66487 / 0.34 ( 6) hydrogen bonds : bond 0.03356 / 2.35 ( 416) hydrogen bonds : angle 4.52179 / 3.13 ( 1158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6575 (mpt180) REVERT: B 63 TRP cc_start: 0.7539 (m100) cc_final: 0.7232 (m100) REVERT: B 75 GLN cc_start: 0.4403 (OUTLIER) cc_final: 0.3266 (tm-30) REVERT: B 222 PHE cc_start: 0.4031 (OUTLIER) cc_final: 0.2528 (m-80) REVERT: B 325 MET cc_start: 0.5757 (tpp) cc_final: 0.4306 (ptt) REVERT: A 18 MET cc_start: 0.6534 (ptp) cc_final: 0.5928 (ptm) REVERT: A 232 LYS cc_start: 0.7720 (ttmt) cc_final: 0.7303 (ttpp) outliers start: 32 outliers final: 23 residues processed: 156 average time/residue: 0.0901 time to fit residues: 19.5643 Evaluate side-chains 148 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [72, 15, 36, 23, 3, 35, 80, 52, 1, 40, 105] chunk 72 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** R 140 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 = 0.4805 r_free = 0.4805 target = 0.235520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.197694 restraints weight = 10392.138| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.16 r_work: 0.4238 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.4101 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8655 Z= 0.180 Angle : 0.618 6.910 11764 Z= 0.322 Chirality : 0.044 0.265 1352 Planarity : 0.004 0.056 1493 Dihedral : 4.474 18.557 1199 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.57 % Allowed : 22.95 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.01 (0.26), residues: 1088 helix: 1.13 (0.27), residues: 383 sheet: -0.11 (0.33), residues: 269 loop : -0.88 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.016 0.002 TYR R 97 PHE 0.015 0.002 PHE R 60 TRP 0.034 0.002 TRP A 129 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 8652) covalent geometry : angle 0.61774 / 0.32 (11758) SS BOND : bond 0.00453 / 0.23 ( 3) SS BOND : angle 0.84537 / 0.43 ( 6) hydrogen bonds : bond 0.03935 / 2.75 ( 416) hydrogen bonds : angle 4.77194 / 3.30 ( 1158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 TRP cc_start: 0.7879 (m100) cc_final: 0.7522 (m100) REVERT: B 75 GLN cc_start: 0.4256 (OUTLIER) cc_final: 0.3227 (tm-30) REVERT: B 220 GLN cc_start: 0.5910 (mp10) cc_final: 0.5618 (mp10) REVERT: B 222 PHE cc_start: 0.4185 (OUTLIER) cc_final: 0.2571 (m-80) REVERT: B 325 MET cc_start: 0.5926 (tpp) cc_final: 0.4158 (ptt) REVERT: A 18 MET cc_start: 0.6524 (ptp) cc_final: 0.6202 (ptm) REVERT: A 145 LYS cc_start: 0.7964 (mmpt) cc_final: 0.7688 (mmtt) REVERT: A 232 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7414 (ttpp) outliers start: 40 outliers final: 33 residues processed: 158 average time/residue: 0.0821 time to fit residues: 18.3457 Evaluate side-chains 156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 154 ASP Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [105, 77, 15, 95, 88, 17, 48, 90, 67, 1, 79] chunk 105 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 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 = 0.4840 r_free = 0.4840 target = 0.239555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.203032 restraints weight = 10207.323| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 2.47 r_work: 0.4290 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8655 Z= 0.116 Angle : 0.564 6.856 11764 Z= 0.295 Chirality : 0.042 0.237 1352 Planarity : 0.004 0.057 1493 Dihedral : 4.197 17.996 1199 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.34 % Allowed : 23.29 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 0.14 (0.26), residues: 1088 helix: 1.33 (0.27), residues: 383 sheet: -0.08 (0.33), residues: 264 loop : -0.84 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.017 0.001 TYR R 324 PHE 0.011 0.001 PHE A 74 TRP 0.043 0.002 TRP A 129 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 8652) covalent geometry : angle 0.56394 / 0.29 (11758) SS BOND : bond 0.00365 / 0.18 ( 3) SS BOND : angle 0.60185 / 0.29 ( 6) hydrogen bonds : bond 0.03361 / 2.36 ( 416) hydrogen bonds : angle 4.52574 / 3.13 ( 1158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6107 (mpt180) REVERT: B 75 GLN cc_start: 0.4174 (OUTLIER) cc_final: 0.3256 (tm-30) REVERT: B 169 TRP cc_start: 0.7994 (OUTLIER) cc_final: 0.7321 (m100) REVERT: B 220 GLN cc_start: 0.5665 (mp10) cc_final: 0.5418 (mp10) REVERT: B 222 PHE cc_start: 0.4129 (OUTLIER) cc_final: 0.2587 (m-80) REVERT: B 325 MET cc_start: 0.5712 (tpp) cc_final: 0.4172 (ptt) REVERT: A 18 MET cc_start: 0.6357 (ptp) cc_final: 0.6002 (ptm) REVERT: A 145 LYS cc_start: 0.7927 (mmpt) cc_final: 0.7712 (mmtt) REVERT: A 232 LYS cc_start: 0.7876 (ttmt) cc_final: 0.7413 (ttpp) REVERT: R 323 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6803 (pt) outliers start: 38 outliers final: 27 residues processed: 155 average time/residue: 0.0826 time to fit residues: 17.9145 Evaluate side-chains 154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 154 ASP Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 275 GLU Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [50, 12, 11, 54, 68, 83, 14, 72, 70, 71, 36] chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 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 = 0.4840 r_free = 0.4840 target = 0.239336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.204139 restraints weight = 10159.646| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 2.02 r_work: 0.4319 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8655 Z= 0.118 Angle : 0.564 7.200 11764 Z= 0.295 Chirality : 0.042 0.249 1352 Planarity : 0.004 0.055 1493 Dihedral : 4.151 17.965 1199 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.77 % Allowed : 23.97 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 0.18 (0.26), residues: 1088 helix: 1.38 (0.27), residues: 382 sheet: -0.13 (0.33), residues: 269 loop : -0.77 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 169 TYR 0.024 0.002 TYR B 85 PHE 0.011 0.001 PHE A 74 TRP 0.045 0.002 TRP A 129 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8652) covalent geometry : angle 0.56413 / 0.29 (11758) SS BOND : bond 0.00409 / 0.20 ( 3) SS BOND : angle 0.68611 / 0.33 ( 6) hydrogen bonds : bond 0.03357 / 2.35 ( 416) hydrogen bonds : angle 4.47872 / 3.10 ( 1158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6012 (mpt180) REVERT: B 75 GLN cc_start: 0.4203 (OUTLIER) cc_final: 0.3270 (tm-30) REVERT: B 169 TRP cc_start: 0.7993 (OUTLIER) cc_final: 0.7388 (m100) REVERT: B 220 GLN cc_start: 0.5723 (mp10) cc_final: 0.5488 (mp10) REVERT: B 222 PHE cc_start: 0.4136 (OUTLIER) cc_final: 0.2602 (m-80) REVERT: B 230 ASN cc_start: 0.5856 (t0) cc_final: 0.5376 (t0) REVERT: B 325 MET cc_start: 0.5812 (tpp) cc_final: 0.4207 (ptp) REVERT: A 18 MET cc_start: 0.6335 (ptp) cc_final: 0.5988 (ptm) REVERT: A 117 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7389 (ptp-110) REVERT: A 142 PHE cc_start: 0.7624 (m-80) cc_final: 0.7380 (m-80) REVERT: A 232 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7426 (ttpp) REVERT: R 60 PHE cc_start: 0.7755 (t80) cc_final: 0.7553 (t80) REVERT: R 323 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6722 (pt) REVERT: S 84 THR cc_start: 0.8093 (m) cc_final: 0.7862 (m) outliers start: 33 outliers final: 25 residues processed: 149 average time/residue: 0.0895 time to fit residues: 18.5241 Evaluate side-chains 146 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 275 GLU Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [95, 66, 93, 92, 4, 103, 68, 23, 82, 43, 46] chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 103 optimal weight: 0.0070 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 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 = 0.4701 r_free = 0.4701 target = 0.231777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.194384 restraints weight = 10275.010| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 2.48 r_work: 0.4212 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8655 Z= 0.113 Angle : 0.557 6.980 11764 Z= 0.290 Chirality : 0.042 0.221 1352 Planarity : 0.004 0.055 1493 Dihedral : 4.112 17.574 1199 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.31 % Allowed : 24.43 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 0.27 (0.27), residues: 1088 helix: 1.47 (0.27), residues: 382 sheet: -0.13 (0.32), residues: 269 loop : -0.72 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 169 TYR 0.025 0.001 TYR B 85 PHE 0.012 0.001 PHE A 74 TRP 0.036 0.002 TRP A 129 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8652) covalent geometry : angle 0.55706 / 0.29 (11758) SS BOND : bond 0.00388 / 0.19 ( 3) SS BOND : angle 0.62279 / 0.30 ( 6) hydrogen bonds : bond 0.03252 / 2.29 ( 416) hydrogen bonds : angle 4.44203 / 3.08 ( 1158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6006 (mpt180) REVERT: B 75 GLN cc_start: 0.4285 (OUTLIER) cc_final: 0.3305 (tm-30) REVERT: B 169 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.7477 (m100) REVERT: B 220 GLN cc_start: 0.5825 (mp10) cc_final: 0.5566 (mp10) REVERT: B 222 PHE cc_start: 0.4009 (OUTLIER) cc_final: 0.2499 (m-80) REVERT: B 230 ASN cc_start: 0.5898 (t0) cc_final: 0.5439 (t0) REVERT: B 325 MET cc_start: 0.5950 (tpp) cc_final: 0.4429 (ptt) REVERT: A 18 MET cc_start: 0.6250 (ptp) cc_final: 0.5902 (ptm) REVERT: A 117 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7573 (ptp-110) REVERT: A 142 PHE cc_start: 0.7574 (m-80) cc_final: 0.7305 (m-80) REVERT: A 145 LYS cc_start: 0.8283 (mmtt) cc_final: 0.8011 (mmmt) REVERT: A 232 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7404 (ttpp) REVERT: R 60 PHE cc_start: 0.7872 (t80) cc_final: 0.7644 (t80) REVERT: R 323 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6764 (pt) REVERT: S 83 MET cc_start: 0.6771 (mtm) cc_final: 0.6452 (mtm) outliers start: 29 outliers final: 23 residues processed: 135 average time/residue: 0.0823 time to fit residues: 15.7990 Evaluate side-chains 134 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 154 ASP Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 275 GLU Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [45, 77, 57, 30, 23, 63, 43, 54, 31, 85, 105] chunk 45 optimal weight: 0.2980 chunk 77 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.231862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.194658 restraints weight = 10264.488| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 2.46 r_work: 0.4210 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8655 Z= 0.113 Angle : 0.552 6.648 11764 Z= 0.287 Chirality : 0.042 0.214 1352 Planarity : 0.004 0.054 1493 Dihedral : 4.087 17.235 1199 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.88 % Allowed : 24.43 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 0.31 (0.27), residues: 1088 helix: 1.52 (0.27), residues: 382 sheet: -0.14 (0.32), residues: 274 loop : -0.67 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 169 TYR 0.022 0.001 TYR B 85 PHE 0.013 0.001 PHE A 74 TRP 0.034 0.002 TRP A 129 HIS 0.005 0.001 HIS R 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8652) covalent geometry : angle 0.55213 / 0.29 (11758) SS BOND : bond 0.00390 / 0.20 ( 3) SS BOND : angle 0.66392 / 0.33 ( 6) hydrogen bonds : bond 0.03261 / 2.29 ( 416) hydrogen bonds : angle 4.44314 / 3.07 ( 1158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.57 seconds wall clock time: 39 minutes 45.78 seconds (2385.78 seconds total)