Starting phenix.real_space_refine on Mon May 12 00:00:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpn_36484/05_2025/8jpn_36484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpn_36484/05_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_36484/05_2025/8jpn_36484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpn_36484/05_2025/8jpn_36484.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpn_36484/05_2025/8jpn_36484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpn_36484/05_2025/8jpn_36484.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASN:plan1': 1, 'ASP:plan': 7} 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: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} 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, 'GLU:plan': 4, 'ARG:plan': 1, '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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3} 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: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 3} 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: 6.33, per 1000 atoms: 0.74 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.24 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: 2.51 Time building geometry restraints manager: 2.67 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: 4.260 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 24.040 Find NCS groups from input model: 0.110 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.000 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (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 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.028 0.002 PHE R 34 TYR 0.014 0.001 TYR R 25 ARG 0.009 0.000 ARG R 99 Details of bonding type rmsd hydrogen bonds : bond 0.14932 ( 457) hydrogen bonds : angle 5.31477 ( 1299) SS BOND : bond 0.00937 ( 4) SS BOND : angle 1.48344 ( 8) covalent geometry : bond 0.00363 ( 8743) covalent geometry : angle 0.60779 (11915) *********************** 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 : 0.926 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: 0.9869 time to fit residues: 205.9794 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 : 0.915 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3743 r_free = 0.3743 target = 0.149770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117248 restraints weight = 10987.508| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.29 r_work: 0.3055 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8747 Z= 0.169 Angle : 0.614 6.738 11923 Z= 0.333 Chirality : 0.044 0.183 1388 Planarity : 0.005 0.049 1514 Dihedral : 4.449 28.395 1246 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.99 % Allowed : 20.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1141 helix: 2.62 (0.26), residues: 391 sheet: 1.26 (0.31), residues: 265 loop : -1.07 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS A 244 PHE 0.022 0.002 PHE R 34 TYR 0.025 0.002 TYR R 277 ARG 0.010 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 457) hydrogen bonds : angle 4.35138 ( 1299) SS BOND : bond 0.01291 ( 4) SS BOND : angle 1.51699 ( 8) covalent geometry : bond 0.00356 ( 8743) covalent geometry : angle 0.61286 (11915) *********************** 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 170 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.903 Fit side-chains REVERT: A 318 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: B 217 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7468 (pmt) REVERT: B 258 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: R 111 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8201 (mm) REVERT: R 131 HIS cc_start: 0.8255 (t-90) cc_final: 0.8000 (t-90) REVERT: R 151 THR cc_start: 0.8091 (m) cc_final: 0.7855 (p) REVERT: R 204 CYS cc_start: 0.8475 (m) cc_final: 0.7965 (m) REVERT: R 208 TYR cc_start: 0.7629 (t80) cc_final: 0.7344 (t80) REVERT: R 285 PHE cc_start: 0.6544 (m-10) cc_final: 0.6322 (m-80) REVERT: S 183 GLN cc_start: 0.8786 (mt0) cc_final: 0.8550 (mt0) outliers start: 42 outliers final: 8 residues processed: 156 average time/residue: 1.0195 time to fit residues: 170.8621 Evaluate side-chains 115 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain S residue 91 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 57 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 0.0000 chunk 23 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111786 restraints weight = 10919.526| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.15 r_work: 0.2930 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8747 Z= 0.165 Angle : 0.602 7.783 11923 Z= 0.321 Chirality : 0.044 0.140 1388 Planarity : 0.004 0.048 1514 Dihedral : 4.273 18.835 1240 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.04 % Allowed : 22.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1141 helix: 2.65 (0.26), residues: 400 sheet: 0.84 (0.30), residues: 281 loop : -1.01 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.002 PHE R 241 TYR 0.012 0.001 TYR R 277 ARG 0.006 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.05612 ( 457) hydrogen bonds : angle 4.27376 ( 1299) SS BOND : bond 0.01471 ( 4) SS BOND : angle 3.41658 ( 8) covalent geometry : bond 0.00335 ( 8743) covalent geometry : angle 0.59605 (11915) *********************** 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 154 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.961 Fit side-chains REVERT: A 20 ASP cc_start: 0.8607 (m-30) cc_final: 0.8361 (m-30) REVERT: A 186 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: B 22 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.5364 (mpt-90) REVERT: B 234 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8732 (t80) REVERT: C 52 THR cc_start: 0.7786 (m) cc_final: 0.7275 (p) REVERT: R 151 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7941 (p) REVERT: R 204 CYS cc_start: 0.8513 (m) cc_final: 0.8053 (m) REVERT: R 209 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7964 (mttt) REVERT: S 183 GLN cc_start: 0.8898 (mt0) cc_final: 0.8675 (mt0) REVERT: S 202 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7276 (mtp180) outliers start: 34 outliers final: 10 residues processed: 136 average time/residue: 1.1966 time to fit residues: 173.4954 Evaluate side-chains 116 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG 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 270 ILE 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 255 ARG Chi-restraints excluded: chain R residue 306 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 49 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 100 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110727 restraints weight = 10936.066| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.22 r_work: 0.2934 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8747 Z= 0.117 Angle : 0.526 5.660 11923 Z= 0.283 Chirality : 0.042 0.141 1388 Planarity : 0.004 0.053 1514 Dihedral : 4.071 19.024 1240 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.21 % Allowed : 22.80 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1141 helix: 2.87 (0.26), residues: 401 sheet: 0.80 (0.30), residues: 277 loop : -0.97 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR R 25 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 457) hydrogen bonds : angle 4.00623 ( 1299) SS BOND : bond 0.00798 ( 4) SS BOND : angle 1.92926 ( 8) covalent geometry : bond 0.00250 ( 8743) covalent geometry : angle 0.52389 (11915) *********************** 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 146 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.862 Fit side-chains REVERT: A 20 ASP cc_start: 0.8605 (m-30) cc_final: 0.8348 (m-30) REVERT: A 186 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 22 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.5356 (mpt-90) REVERT: B 227 SER cc_start: 0.9442 (m) cc_final: 0.9137 (t) REVERT: B 234 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8880 (t80) REVERT: B 258 ASP cc_start: 0.8246 (t0) cc_final: 0.7962 (t0) REVERT: R 151 THR cc_start: 0.8249 (m) cc_final: 0.8027 (p) REVERT: R 209 LYS cc_start: 0.8302 (mtpp) cc_final: 0.8059 (mttt) outliers start: 27 outliers final: 12 residues processed: 135 average time/residue: 1.1222 time to fit residues: 161.9213 Evaluate side-chains 121 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG 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 270 ILE Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 103 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN R 301 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107488 restraints weight = 10687.736| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.11 r_work: 0.2813 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8747 Z= 0.163 Angle : 0.602 7.784 11923 Z= 0.319 Chirality : 0.044 0.145 1388 Planarity : 0.004 0.056 1514 Dihedral : 4.321 18.767 1240 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.56 % Allowed : 22.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1141 helix: 2.81 (0.26), residues: 397 sheet: 0.81 (0.30), residues: 275 loop : -1.07 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS R 301 PHE 0.023 0.002 PHE R 34 TYR 0.012 0.001 TYR R 107 ARG 0.002 0.000 ARG R 120 Details of bonding type rmsd hydrogen bonds : bond 0.05653 ( 457) hydrogen bonds : angle 4.21022 ( 1299) SS BOND : bond 0.01241 ( 4) SS BOND : angle 2.15659 ( 8) covalent geometry : bond 0.00372 ( 8743) covalent geometry : angle 0.59949 (11915) *********************** 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 143 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.883 Fit side-chains REVERT: A 20 ASP cc_start: 0.8583 (m-30) cc_final: 0.8346 (m-30) REVERT: A 186 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: B 22 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.5191 (mpt-90) REVERT: B 227 SER cc_start: 0.9477 (m) cc_final: 0.9158 (t) REVERT: B 234 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8813 (t80) REVERT: R 151 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7984 (p) REVERT: R 214 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7171 (mp) outliers start: 30 outliers final: 11 residues processed: 133 average time/residue: 1.1027 time to fit residues: 156.9188 Evaluate side-chains 127 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE 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 151 THR Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 chunk 27 optimal weight: 0.0470 chunk 100 optimal weight: 0.6980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110364 restraints weight = 10731.786| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.13 r_work: 0.2916 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8747 Z= 0.112 Angle : 0.520 6.905 11923 Z= 0.279 Chirality : 0.042 0.142 1388 Planarity : 0.004 0.055 1514 Dihedral : 4.046 18.527 1240 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.21 % Allowed : 23.63 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1141 helix: 2.92 (0.26), residues: 403 sheet: 0.78 (0.30), residues: 278 loop : -0.93 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE R 34 TYR 0.018 0.001 TYR R 25 ARG 0.007 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 457) hydrogen bonds : angle 3.99872 ( 1299) SS BOND : bond 0.00717 ( 4) SS BOND : angle 1.38639 ( 8) covalent geometry : bond 0.00237 ( 8743) covalent geometry : angle 0.51906 (11915) *********************** 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 149 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.872 Fit side-chains REVERT: A 285 ILE cc_start: 0.8178 (mm) cc_final: 0.7964 (mt) REVERT: B 22 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.5061 (mpt-90) REVERT: B 227 SER cc_start: 0.9456 (m) cc_final: 0.9181 (t) REVERT: B 234 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8801 (t80) REVERT: C 52 THR cc_start: 0.7950 (m) cc_final: 0.7560 (p) outliers start: 27 outliers final: 10 residues processed: 142 average time/residue: 1.1336 time to fit residues: 172.0589 Evaluate side-chains 124 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 70 LEU 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 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.140709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108003 restraints weight = 10809.032| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.23 r_work: 0.2874 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8747 Z= 0.137 Angle : 0.569 7.174 11923 Z= 0.302 Chirality : 0.043 0.142 1388 Planarity : 0.004 0.056 1514 Dihedral : 4.162 18.434 1240 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.44 % Allowed : 23.16 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1141 helix: 2.86 (0.26), residues: 405 sheet: 0.82 (0.30), residues: 277 loop : -0.98 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE R 34 TYR 0.019 0.001 TYR R 126 ARG 0.006 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 457) hydrogen bonds : angle 4.06794 ( 1299) SS BOND : bond 0.01013 ( 4) SS BOND : angle 1.72029 ( 8) covalent geometry : bond 0.00307 ( 8743) covalent geometry : angle 0.56749 (11915) *********************** 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 146 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.872 Fit side-chains REVERT: A 20 ASP cc_start: 0.8555 (m-30) cc_final: 0.8341 (m-30) REVERT: A 285 ILE cc_start: 0.8245 (mm) cc_final: 0.8019 (mt) REVERT: B 22 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.4879 (mpt-90) REVERT: B 217 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8181 (pmt) REVERT: B 227 SER cc_start: 0.9463 (m) cc_final: 0.9179 (t) REVERT: B 234 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.8833 (t80) REVERT: R 214 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7250 (mp) REVERT: S 157 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8388 (mm) outliers start: 29 outliers final: 15 residues processed: 138 average time/residue: 1.0489 time to fit residues: 155.6278 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 : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 181 THR 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 270 ILE 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 80 ILE Chi-restraints excluded: chain R residue 94 LEU 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 R residue 306 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 157 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 27 optimal weight: 0.0060 chunk 48 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.142438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109432 restraints weight = 10840.657| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.25 r_work: 0.2891 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.7040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8747 Z= 0.114 Angle : 0.526 6.439 11923 Z= 0.281 Chirality : 0.042 0.144 1388 Planarity : 0.004 0.056 1514 Dihedral : 4.033 18.291 1240 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.61 % Allowed : 24.35 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1141 helix: 2.99 (0.26), residues: 405 sheet: 0.84 (0.30), residues: 278 loop : -0.93 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.029 0.001 PHE R 34 TYR 0.019 0.001 TYR R 25 ARG 0.006 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 457) hydrogen bonds : angle 3.98427 ( 1299) SS BOND : bond 0.00751 ( 4) SS BOND : angle 1.31263 ( 8) covalent geometry : bond 0.00243 ( 8743) covalent geometry : angle 0.52533 (11915) *********************** 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 140 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.892 Fit side-chains REVERT: A 229 ASP cc_start: 0.8733 (m-30) cc_final: 0.8408 (t0) REVERT: A 285 ILE cc_start: 0.8310 (mm) cc_final: 0.8076 (mt) REVERT: B 217 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8153 (pmt) REVERT: B 227 SER cc_start: 0.9451 (m) cc_final: 0.9184 (t) REVERT: B 234 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8787 (t80) REVERT: R 214 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7201 (mp) outliers start: 22 outliers final: 14 residues processed: 136 average time/residue: 1.0852 time to fit residues: 157.9827 Evaluate side-chains 133 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 70 LEU 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 94 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.141405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108689 restraints weight = 10841.450| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.23 r_work: 0.2896 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8747 Z= 0.125 Angle : 0.562 12.805 11923 Z= 0.295 Chirality : 0.042 0.144 1388 Planarity : 0.004 0.056 1514 Dihedral : 4.043 18.191 1240 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.26 % Allowed : 25.30 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1141 helix: 2.97 (0.26), residues: 405 sheet: 0.87 (0.30), residues: 277 loop : -0.92 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.001 PHE R 34 TYR 0.018 0.001 TYR R 126 ARG 0.007 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 457) hydrogen bonds : angle 4.00869 ( 1299) SS BOND : bond 0.00921 ( 4) SS BOND : angle 1.53447 ( 8) covalent geometry : bond 0.00276 ( 8743) covalent geometry : angle 0.56064 (11915) *********************** 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: 19 poor density : 120 time to evaluate : 0.997 Fit side-chains REVERT: A 285 ILE cc_start: 0.8363 (mm) cc_final: 0.8118 (mt) REVERT: B 217 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8215 (pmt) REVERT: B 227 SER cc_start: 0.9454 (m) cc_final: 0.9187 (t) REVERT: B 234 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8804 (t80) REVERT: R 214 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7282 (mp) outliers start: 19 outliers final: 13 residues processed: 135 average time/residue: 1.1730 time to fit residues: 169.0274 Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 70 LEU 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 94 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106588 restraints weight = 10752.290| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.08 r_work: 0.2806 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8747 Z= 0.169 Angle : 0.626 13.779 11923 Z= 0.327 Chirality : 0.044 0.147 1388 Planarity : 0.004 0.058 1514 Dihedral : 4.320 19.383 1240 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.26 % Allowed : 25.06 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1141 helix: 2.79 (0.26), residues: 405 sheet: 0.81 (0.30), residues: 277 loop : -0.99 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.022 0.002 PHE R 34 TYR 0.022 0.002 TYR R 25 ARG 0.006 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.05558 ( 457) hydrogen bonds : angle 4.19384 ( 1299) SS BOND : bond 0.01141 ( 4) SS BOND : angle 1.88135 ( 8) covalent geometry : bond 0.00392 ( 8743) covalent geometry : angle 0.62384 (11915) ********************** 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 131 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.897 Fit side-chains REVERT: A 20 ASP cc_start: 0.8593 (m-30) cc_final: 0.8342 (m-30) REVERT: A 285 ILE cc_start: 0.8424 (mm) cc_final: 0.8150 (mt) REVERT: B 217 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8156 (pmt) REVERT: B 227 SER cc_start: 0.9454 (m) cc_final: 0.9171 (t) REVERT: B 234 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8825 (t80) REVERT: R 214 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7426 (mp) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 1.0859 time to fit residues: 150.1289 Evaluate side-chains 124 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108798 restraints weight = 10859.121| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.12 r_work: 0.2860 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.7298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8747 Z= 0.125 Angle : 0.566 12.911 11923 Z= 0.298 Chirality : 0.042 0.144 1388 Planarity : 0.004 0.057 1514 Dihedral : 4.141 18.150 1240 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.38 % Allowed : 24.58 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1141 helix: 2.89 (0.26), residues: 404 sheet: 0.79 (0.30), residues: 280 loop : -0.98 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.023 0.001 PHE R 34 TYR 0.012 0.001 TYR R 90 ARG 0.006 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 457) hydrogen bonds : angle 4.07057 ( 1299) SS BOND : bond 0.00848 ( 4) SS BOND : angle 1.49847 ( 8) covalent geometry : bond 0.00274 ( 8743) covalent geometry : angle 0.56515 (11915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6966.81 seconds wall clock time: 120 minutes 46.23 seconds (7246.23 seconds total)