Starting phenix.real_space_refine on Fri Aug 22 23:23:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpn_36484/08_2025/8jpn_36484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpn_36484/08_2025/8jpn_36484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpn_36484/08_2025/8jpn_36484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpn_36484/08_2025/8jpn_36484.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpn_36484/08_2025/8jpn_36484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpn_36484/08_2025/8jpn_36484.cif" } resolution = 2.9 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= -0.001 sd= 0.049 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 52 5.16 5 C 5469 2.51 5 N 1447 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8557 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2528 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 336} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 7, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 397 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2187 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 6, 'TYR:plan': 3, 'PHE:plan': 4, 'ASP:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 129 Chain: "S" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1723 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'U9S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.17, per 1000 atoms: 0.25 Number of scatterers: 8557 At special positions: 0 Unit cell: (90.316, 124.69, 130.756, 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 52 16.00 O 1589 8.00 N 1447 7.00 C 5469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 268 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 172 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.05 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: 0.73 Conformation dependent library (CDL) restraints added in 450.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 39.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.632A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.338A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.508A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.790A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.597A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 11 through 51 removed outlier: 4.827A pdb=" N LEU R 26 " --> pdb=" O GLU R 22 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER R 27 " --> pdb=" O LYS R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 74 Processing helix chain 'R' and resid 76 through 86 Processing helix chain 'R' and resid 91 through 126 removed outlier: 3.897A pdb=" N TYR R 100 " --> pdb=" O ILE R 96 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL R 101 " --> pdb=" O SER R 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 102 " --> pdb=" O ASN R 98 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS R 103 " --> pdb=" O ARG R 99 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 134 Processing helix chain 'R' and resid 135 through 155 Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 174 through 178 Processing helix chain 'R' and resid 180 through 196 Processing helix chain 'R' and resid 196 through 220 Processing helix chain 'R' and resid 227 through 259 removed outlier: 3.725A pdb=" N LEU R 231 " --> pdb=" O LEU R 227 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 247 - end of helix removed outlier: 3.607A pdb=" N ARG R 259 " --> pdb=" O ARG R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 285 removed outlier: 3.669A pdb=" N ASN R 274 " --> pdb=" O GLN R 270 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR R 280 " --> pdb=" O PHE R 276 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG R 281 " --> pdb=" O TYR R 277 " (cutoff:3.500A) Proline residue: R 282 - end of helix removed outlier: 3.841A pdb=" N PHE R 285 " --> pdb=" O ARG R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 296 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 312 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.525A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.639A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.702A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.934A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.006A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.691A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.979A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.582A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.694A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (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: 6.016A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.016A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.562A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1299 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: 1.55 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2763 1.34 - 1.46: 2216 1.46 - 1.58: 3690 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 8743 Sorted by residual: bond pdb=" N VAL R 289 " pdb=" CA VAL R 289 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.04e+00 bond pdb=" N SER R 288 " pdb=" CA SER R 288 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.33e-02 5.65e+03 5.63e+00 bond pdb=" C04 U9S R 501 " pdb=" C05 U9S R 501 " ideal model delta sigma weight residual 1.466 1.504 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" N LEU S 219 " pdb=" CA LEU S 219 " ideal model delta sigma weight residual 1.456 1.480 -0.024 1.27e-02 6.20e+03 3.52e+00 bond pdb=" N ARG S 218 " pdb=" CA ARG S 218 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.33e+00 ... (remaining 8738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11716 1.94 - 3.88: 168 3.88 - 5.82: 25 5.82 - 7.76: 5 7.76 - 9.70: 1 Bond angle restraints: 11915 Sorted by residual: angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N ALA A 41 " ideal model delta sigma weight residual 114.58 117.46 -2.88 8.60e-01 1.35e+00 1.12e+01 angle pdb=" N SER R 288 " pdb=" CA SER R 288 " pdb=" C SER R 288 " ideal model delta sigma weight residual 113.28 109.26 4.02 1.22e+00 6.72e-01 1.09e+01 angle pdb=" CB MET R 251 " pdb=" CG MET R 251 " pdb=" SD MET R 251 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C SER S 217 " pdb=" N ARG S 218 " pdb=" CA ARG S 218 " ideal model delta sigma weight residual 121.54 115.82 5.72 1.91e+00 2.74e-01 8.97e+00 angle pdb=" CA CYS S 96 " pdb=" CB CYS S 96 " pdb=" SG CYS S 96 " ideal model delta sigma weight residual 114.40 120.79 -6.39 2.30e+00 1.89e-01 7.73e+00 ... (remaining 11910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 4490 17.06 - 34.13: 454 34.13 - 51.19: 133 51.19 - 68.25: 21 68.25 - 85.32: 9 Dihedral angle restraints: 5107 sinusoidal: 1746 harmonic: 3361 Sorted by residual: dihedral pdb=" CB CYS R 11 " pdb=" SG CYS R 11 " pdb=" SG CYS R 268 " pdb=" CB CYS R 268 " ideal model delta sinusoidal sigma weight residual -86.00 -47.23 -38.77 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 808 0.030 - 0.059: 360 0.059 - 0.089: 131 0.089 - 0.118: 73 0.118 - 0.148: 16 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA VAL R 289 " pdb=" N VAL R 289 " pdb=" C VAL R 289 " pdb=" CB VAL R 289 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA PRO S 236 " pdb=" N PRO S 236 " pdb=" C PRO S 236 " pdb=" CB PRO S 236 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1385 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO S 75 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO B 236 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP R 119 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" CG ASP R 119 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP R 119 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP R 119 " -0.010 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2107 2.79 - 3.32: 7395 3.32 - 3.85: 13568 3.85 - 4.37: 16028 4.37 - 4.90: 28748 Nonbonded interactions: 67846 Sorted by model distance: nonbonded pdb=" O ALA R 104 " pdb=" OG1 THR R 108 " model vdw 2.268 3.040 nonbonded pdb=" O VAL R 272 " pdb=" OG SER R 275 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.298 3.040 nonbonded pdb=" OE1 GLU S 6 " pdb=" N GLY S 114 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.333 3.120 ... (remaining 67841 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8747 Z= 0.170 Angle : 0.609 9.704 11923 Z= 0.335 Chirality : 0.043 0.148 1388 Planarity : 0.004 0.067 1514 Dihedral : 15.560 85.318 2929 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.36 % Allowed : 20.90 % Favored : 78.74 % 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 aren not related in a simple way. whole: 1.11 (0.25), residues: 1141 helix: 2.43 (0.27), residues: 389 sheet: 1.04 (0.30), residues: 277 loop : -0.94 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 99 TYR 0.014 0.001 TYR R 25 PHE 0.028 0.002 PHE R 34 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8743) covalent geometry : angle 0.60779 (11915) SS BOND : bond 0.00937 ( 4) SS BOND : angle 1.48344 ( 8) hydrogen bonds : bond 0.14932 ( 457) hydrogen bonds : angle 5.31477 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 0.363 Fit side-chains REVERT: A 293 SER cc_start: 0.7508 (m) cc_final: 0.7123 (m) REVERT: B 212 ASP cc_start: 0.5923 (t0) cc_final: 0.5644 (t70) REVERT: R 151 THR cc_start: 0.7725 (m) cc_final: 0.7501 (p) REVERT: R 204 CYS cc_start: 0.7966 (m) cc_final: 0.7513 (m) REVERT: R 208 TYR cc_start: 0.7321 (t80) cc_final: 0.7010 (t80) outliers start: 3 outliers final: 3 residues processed: 194 average time/residue: 0.5210 time to fit residues: 108.1089 Evaluate side-chains 117 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 73 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 259 GLN R 287 ASN S 113 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113455 restraints weight = 10945.442| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.23 r_work: 0.2978 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 8747 Z= 0.224 Angle : 0.705 8.916 11923 Z= 0.380 Chirality : 0.048 0.242 1388 Planarity : 0.005 0.055 1514 Dihedral : 4.852 30.688 1246 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.11 % Allowed : 19.00 % Favored : 75.89 % 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 aren not related in a simple way. whole: 0.94 (0.25), residues: 1141 helix: 2.29 (0.26), residues: 396 sheet: 1.03 (0.30), residues: 281 loop : -1.18 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.023 0.002 TYR R 277 PHE 0.019 0.002 PHE R 241 TRP 0.017 0.002 TRP B 211 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 8743) covalent geometry : angle 0.70359 (11915) SS BOND : bond 0.03284 ( 4) SS BOND : angle 1.56000 ( 8) hydrogen bonds : bond 0.06145 ( 457) hydrogen bonds : angle 4.52638 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.351 Fit side-chains REVERT: A 318 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: B 234 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8873 (t80) REVERT: B 258 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7661 (t70) REVERT: R 151 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7890 (p) REVERT: R 204 CYS cc_start: 0.8513 (m) cc_final: 0.8034 (m) REVERT: R 209 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7991 (mttt) REVERT: S 183 GLN cc_start: 0.8923 (mt0) cc_final: 0.8686 (mt0) REVERT: S 202 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7504 (mtp180) outliers start: 43 outliers final: 14 residues processed: 159 average time/residue: 0.5675 time to fit residues: 96.1450 Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 308 ASN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.0040 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 45 optimal weight: 0.0980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN R 134 GLN R 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113561 restraints weight = 10894.474| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.08 r_work: 0.2988 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8747 Z= 0.111 Angle : 0.515 5.757 11923 Z= 0.279 Chirality : 0.042 0.146 1388 Planarity : 0.004 0.051 1514 Dihedral : 4.229 23.159 1242 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.09 % Allowed : 22.09 % Favored : 74.82 % 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 aren not related in a simple way. whole: 1.16 (0.25), residues: 1141 helix: 2.73 (0.26), residues: 394 sheet: 0.91 (0.30), residues: 281 loop : -1.11 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.013 0.001 TYR S 190 PHE 0.014 0.001 PHE B 199 TRP 0.009 0.001 TRP B 211 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8743) covalent geometry : angle 0.51048 (11915) SS BOND : bond 0.01108 ( 4) SS BOND : angle 2.53012 ( 8) hydrogen bonds : bond 0.04536 ( 457) hydrogen bonds : angle 4.13237 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.298 Fit side-chains REVERT: A 186 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: B 217 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8152 (pmt) REVERT: B 234 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8908 (t80) REVERT: B 254 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8224 (t0) REVERT: C 52 THR cc_start: 0.7610 (m) cc_final: 0.7108 (p) REVERT: R 151 THR cc_start: 0.8200 (m) cc_final: 0.7950 (p) REVERT: R 204 CYS cc_start: 0.8482 (m) cc_final: 0.8019 (m) REVERT: S 3 GLN cc_start: 0.8213 (mt0) cc_final: 0.7992 (mm-40) REVERT: S 11 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7199 (mp) REVERT: S 183 GLN cc_start: 0.8892 (mt0) cc_final: 0.8682 (mt0) outliers start: 26 outliers final: 5 residues processed: 126 average time/residue: 0.5150 time to fit residues: 69.4862 Evaluate side-chains 111 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 76 optimal weight: 0.0060 chunk 37 optimal weight: 0.0470 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109534 restraints weight = 11124.009| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.09 r_work: 0.3019 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8747 Z= 0.102 Angle : 0.489 5.489 11923 Z= 0.263 Chirality : 0.041 0.143 1388 Planarity : 0.004 0.051 1514 Dihedral : 3.888 18.492 1240 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.38 % Allowed : 23.87 % Favored : 73.75 % 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 aren not related in a simple way. whole: 1.37 (0.25), residues: 1141 helix: 2.93 (0.26), residues: 400 sheet: 0.84 (0.29), residues: 284 loop : -0.96 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.018 0.001 TYR R 25 PHE 0.011 0.001 PHE B 199 TRP 0.008 0.001 TRP B 211 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8743) covalent geometry : angle 0.48802 (11915) SS BOND : bond 0.00670 ( 4) SS BOND : angle 1.52616 ( 8) hydrogen bonds : bond 0.03995 ( 457) hydrogen bonds : angle 3.90925 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.367 Fit side-chains REVERT: B 234 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8882 (t80) REVERT: B 254 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8219 (t0) REVERT: C 52 THR cc_start: 0.7725 (m) cc_final: 0.7267 (p) REVERT: R 151 THR cc_start: 0.8217 (m) cc_final: 0.7998 (p) outliers start: 20 outliers final: 10 residues processed: 132 average time/residue: 0.5331 time to fit residues: 75.0633 Evaluate side-chains 119 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 93 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108919 restraints weight = 10865.267| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.47 r_work: 0.2911 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8747 Z= 0.140 Angle : 0.566 6.946 11923 Z= 0.301 Chirality : 0.043 0.139 1388 Planarity : 0.004 0.054 1514 Dihedral : 4.130 18.789 1240 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.09 % Allowed : 22.80 % Favored : 74.11 % 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 aren not related in a simple way. whole: 1.33 (0.25), residues: 1141 helix: 2.89 (0.26), residues: 401 sheet: 0.85 (0.30), residues: 283 loop : -1.00 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.011 0.001 TYR S 190 PHE 0.025 0.002 PHE R 34 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8743) covalent geometry : angle 0.56370 (11915) SS BOND : bond 0.01095 ( 4) SS BOND : angle 1.89147 ( 8) hydrogen bonds : bond 0.05086 ( 457) hydrogen bonds : angle 4.07887 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.308 Fit side-chains REVERT: A 20 ASP cc_start: 0.8631 (m-30) cc_final: 0.8358 (m-30) REVERT: A 186 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: B 217 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8432 (pmt) REVERT: B 227 SER cc_start: 0.9466 (m) cc_final: 0.9167 (t) REVERT: B 234 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8900 (t80) REVERT: B 254 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8387 (t0) REVERT: C 52 THR cc_start: 0.8079 (m) cc_final: 0.7680 (p) REVERT: R 151 THR cc_start: 0.8284 (m) cc_final: 0.8058 (p) REVERT: R 209 LYS cc_start: 0.8380 (mtpp) cc_final: 0.8133 (mttt) outliers start: 26 outliers final: 12 residues processed: 134 average time/residue: 0.5466 time to fit residues: 78.1405 Evaluate side-chains 139 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN R 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106995 restraints weight = 10752.455| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.19 r_work: 0.2873 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8747 Z= 0.161 Angle : 0.595 7.346 11923 Z= 0.318 Chirality : 0.044 0.150 1388 Planarity : 0.004 0.056 1514 Dihedral : 4.370 18.830 1240 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.44 % Allowed : 22.68 % Favored : 73.87 % 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 aren not related in a simple way. whole: 1.20 (0.25), residues: 1141 helix: 2.74 (0.26), residues: 404 sheet: 0.84 (0.30), residues: 277 loop : -1.08 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 62 TYR 0.021 0.002 TYR R 25 PHE 0.013 0.002 PHE R 241 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8743) covalent geometry : angle 0.59289 (11915) SS BOND : bond 0.01146 ( 4) SS BOND : angle 1.87938 ( 8) hydrogen bonds : bond 0.05578 ( 457) hydrogen bonds : angle 4.17647 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.368 Fit side-chains REVERT: A 20 ASP cc_start: 0.8605 (m-30) cc_final: 0.8319 (m-30) REVERT: A 186 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 285 ILE cc_start: 0.8230 (mm) cc_final: 0.8001 (mt) REVERT: B 227 SER cc_start: 0.9483 (m) cc_final: 0.9192 (t) REVERT: B 234 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8840 (t80) REVERT: B 254 ASP cc_start: 0.8705 (p0) cc_final: 0.8435 (t70) REVERT: R 214 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7414 (mp) REVERT: S 3 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8431 (mt0) REVERT: S 144 THR cc_start: 0.7853 (m) cc_final: 0.7362 (t) REVERT: S 202 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7934 (mtp180) outliers start: 29 outliers final: 17 residues processed: 144 average time/residue: 0.5732 time to fit residues: 88.0123 Evaluate side-chains 132 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103362 restraints weight = 10911.405| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.70 r_work: 0.2729 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.7231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 8747 Z= 0.270 Angle : 0.739 9.755 11923 Z= 0.389 Chirality : 0.049 0.198 1388 Planarity : 0.005 0.060 1514 Dihedral : 4.864 25.511 1240 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.80 % Allowed : 21.62 % Favored : 74.58 % 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 aren not related in a simple way. whole: 0.79 (0.25), residues: 1141 helix: 2.40 (0.26), residues: 396 sheet: 0.59 (0.30), residues: 286 loop : -1.26 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.015 0.002 TYR S 103 PHE 0.022 0.002 PHE R 241 TRP 0.017 0.002 TRP B 82 HIS 0.008 0.002 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 8743) covalent geometry : angle 0.73595 (11915) SS BOND : bond 0.01644 ( 4) SS BOND : angle 2.58277 ( 8) hydrogen bonds : bond 0.07284 ( 457) hydrogen bonds : angle 4.54631 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.264 Fit side-chains REVERT: A 186 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: B 217 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8311 (pmt) REVERT: B 227 SER cc_start: 0.9479 (m) cc_final: 0.9149 (t) REVERT: B 234 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8919 (t80) REVERT: B 254 ASP cc_start: 0.8785 (p0) cc_final: 0.8380 (t0) REVERT: R 214 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7690 (mp) REVERT: S 3 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8449 (mt0) REVERT: S 144 THR cc_start: 0.8031 (m) cc_final: 0.7563 (t) outliers start: 32 outliers final: 17 residues processed: 139 average time/residue: 0.5468 time to fit residues: 81.2128 Evaluate side-chains 132 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 57 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 134 GLN Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108319 restraints weight = 10880.858| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.12 r_work: 0.2900 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.7277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8747 Z= 0.119 Angle : 0.550 8.262 11923 Z= 0.295 Chirality : 0.042 0.144 1388 Planarity : 0.004 0.056 1514 Dihedral : 4.316 19.949 1240 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.49 % Allowed : 22.57 % Favored : 74.94 % 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 aren not related in a simple way. whole: 1.18 (0.25), residues: 1141 helix: 2.79 (0.26), residues: 401 sheet: 0.73 (0.30), residues: 288 loop : -1.09 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 62 TYR 0.017 0.001 TYR R 25 PHE 0.027 0.001 PHE R 34 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8743) covalent geometry : angle 0.54844 (11915) SS BOND : bond 0.00798 ( 4) SS BOND : angle 1.45526 ( 8) hydrogen bonds : bond 0.04851 ( 457) hydrogen bonds : angle 4.12988 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.348 Fit side-chains REVERT: A 20 ASP cc_start: 0.8574 (m-30) cc_final: 0.8318 (m-30) REVERT: B 227 SER cc_start: 0.9472 (m) cc_final: 0.9205 (t) REVERT: B 234 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8935 (t80) REVERT: B 254 ASP cc_start: 0.8683 (p0) cc_final: 0.8427 (t70) REVERT: S 3 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8401 (mt0) outliers start: 21 outliers final: 10 residues processed: 138 average time/residue: 0.5736 time to fit residues: 84.0809 Evaluate side-chains 127 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 86 optimal weight: 0.0970 chunk 18 optimal weight: 0.0170 chunk 71 optimal weight: 1.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108843 restraints weight = 10820.479| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.24 r_work: 0.2915 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8747 Z= 0.118 Angle : 0.553 13.094 11923 Z= 0.292 Chirality : 0.042 0.143 1388 Planarity : 0.004 0.054 1514 Dihedral : 4.106 18.328 1240 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.78 % Allowed : 23.40 % Favored : 74.82 % 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 aren not related in a simple way. whole: 1.31 (0.25), residues: 1141 helix: 2.92 (0.26), residues: 403 sheet: 0.69 (0.29), residues: 292 loop : -1.00 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.013 0.001 TYR S 190 PHE 0.023 0.001 PHE R 34 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8743) covalent geometry : angle 0.55138 (11915) SS BOND : bond 0.00799 ( 4) SS BOND : angle 1.53413 ( 8) hydrogen bonds : bond 0.04578 ( 457) hydrogen bonds : angle 3.99532 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.386 Fit side-chains REVERT: B 227 SER cc_start: 0.9464 (m) cc_final: 0.9203 (t) REVERT: B 234 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8891 (t80) REVERT: B 254 ASP cc_start: 0.8643 (p0) cc_final: 0.8421 (t70) outliers start: 15 outliers final: 7 residues processed: 137 average time/residue: 0.5601 time to fit residues: 81.3993 Evaluate side-chains 126 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 0.0870 chunk 60 optimal weight: 0.0050 chunk 83 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110746 restraints weight = 10868.470| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.26 r_work: 0.2951 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.7359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8747 Z= 0.107 Angle : 0.531 13.196 11923 Z= 0.280 Chirality : 0.041 0.144 1388 Planarity : 0.004 0.053 1514 Dihedral : 3.976 18.192 1240 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.31 % Allowed : 24.35 % Favored : 74.35 % 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 aren not related in a simple way. whole: 1.38 (0.25), residues: 1141 helix: 2.96 (0.26), residues: 404 sheet: 0.74 (0.29), residues: 292 loop : -0.95 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.019 0.001 TYR R 25 PHE 0.023 0.001 PHE R 34 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8743) covalent geometry : angle 0.52989 (11915) SS BOND : bond 0.00705 ( 4) SS BOND : angle 1.30622 ( 8) hydrogen bonds : bond 0.04127 ( 457) hydrogen bonds : angle 3.94522 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.295 Fit side-chains REVERT: B 227 SER cc_start: 0.9453 (m) cc_final: 0.9196 (t) REVERT: B 234 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8823 (t80) REVERT: B 254 ASP cc_start: 0.8592 (p0) cc_final: 0.8381 (t70) REVERT: R 203 MET cc_start: 0.8419 (ttp) cc_final: 0.8075 (mtp) outliers start: 11 outliers final: 5 residues processed: 127 average time/residue: 0.6132 time to fit residues: 82.8100 Evaluate side-chains 123 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109586 restraints weight = 10798.383| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.24 r_work: 0.2933 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.7369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8747 Z= 0.116 Angle : 0.548 13.321 11923 Z= 0.288 Chirality : 0.042 0.142 1388 Planarity : 0.004 0.054 1514 Dihedral : 3.988 18.155 1240 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.43 % Allowed : 24.23 % Favored : 74.35 % 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 aren not related in a simple way. whole: 1.39 (0.25), residues: 1141 helix: 2.95 (0.26), residues: 404 sheet: 0.74 (0.30), residues: 292 loop : -0.93 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.013 0.001 TYR S 190 PHE 0.022 0.001 PHE R 34 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8743) covalent geometry : angle 0.54681 (11915) SS BOND : bond 0.00828 ( 4) SS BOND : angle 1.45719 ( 8) hydrogen bonds : bond 0.04353 ( 457) hydrogen bonds : angle 3.94735 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3599.98 seconds wall clock time: 62 minutes 2.19 seconds (3722.19 seconds total)