Starting phenix.real_space_refine on Wed Sep 17 11:05:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zf6_60051/09_2025/8zf6_60051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zf6_60051/09_2025/8zf6_60051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zf6_60051/09_2025/8zf6_60051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zf6_60051/09_2025/8zf6_60051.map" model { file = "/net/cci-nas-00/data/ceres_data/8zf6_60051/09_2025/8zf6_60051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zf6_60051/09_2025/8zf6_60051_neut.cif" } resolution = 2.98 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5264 2.51 5 N 1438 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8284 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1865 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2484 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 85 Chain: "G" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 355 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1888 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 254} Chain breaks: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 14, 'ASP:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 133 Chain: "S" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1692 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 2.37, per 1000 atoms: 0.29 Number of scatterers: 8284 At special positions: 0 Unit cell: (86.92, 124.02, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1529 8.00 N 1438 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 525.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 removed outlier: 3.639A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.615A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.606A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.518A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 18 through 47 removed outlier: 4.559A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 79 removed outlier: 4.125A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 121 removed outlier: 4.008A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 125 removed outlier: 3.915A pdb=" N PHE R 125 " --> pdb=" O PRO R 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 122 through 125' Processing helix chain 'R' and resid 129 through 150 removed outlier: 3.774A pdb=" N SER R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.648A pdb=" N GLY R 155 " --> pdb=" O PRO R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 191 removed outlier: 3.708A pdb=" N ALA R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 209 removed outlier: 3.588A pdb=" N LEU R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 253 removed outlier: 3.538A pdb=" N VAL R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) Proline residue: R 231 - end of helix Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 266 through 284 Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 287 through 295 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.226A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.732A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.156A 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 helix chain 'S' and resid 220 through 224 removed outlier: 3.941A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.614A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.581A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.756A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.564A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.712A 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: 6.614A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.101A 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: 6.863A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.517A 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: 6.602A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.388A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 158 through 159 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.579A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.014A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.539A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.635A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1254 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: 1.28 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1338 1.29 - 1.42: 2329 1.42 - 1.56: 4729 1.56 - 1.69: 2 1.69 - 1.82: 73 Bond restraints: 8471 Sorted by residual: bond pdb=" C HIS A 387 " pdb=" O HIS A 387 " ideal model delta sigma weight residual 1.237 1.156 0.081 1.17e-02 7.31e+03 4.75e+01 bond pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 1.523 1.435 0.089 1.30e-02 5.92e+03 4.67e+01 bond pdb=" CA HIS A 387 " pdb=" C HIS A 387 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.30e-02 5.92e+03 4.36e+01 bond pdb=" CA ALA A 39 " pdb=" C ALA A 39 " ideal model delta sigma weight residual 1.523 1.439 0.084 1.28e-02 6.10e+03 4.33e+01 bond pdb=" CA HIS A 387 " pdb=" CB HIS A 387 " ideal model delta sigma weight residual 1.528 1.433 0.096 1.56e-02 4.11e+03 3.77e+01 ... (remaining 8466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11177 1.88 - 3.76: 294 3.76 - 5.63: 57 5.63 - 7.51: 16 7.51 - 9.39: 6 Bond angle restraints: 11550 Sorted by residual: angle pdb=" N GLN S 183 " pdb=" CA GLN S 183 " pdb=" C GLN S 183 " ideal model delta sigma weight residual 110.41 119.80 -9.39 1.23e+00 6.61e-01 5.83e+01 angle pdb=" C SER S 184 " pdb=" N PRO S 185 " pdb=" CA PRO S 185 " ideal model delta sigma weight residual 119.78 125.62 -5.84 1.03e+00 9.43e-01 3.22e+01 angle pdb=" C GLN A 384 " pdb=" CA GLN A 384 " pdb=" CB GLN A 384 " ideal model delta sigma weight residual 110.79 101.75 9.04 1.66e+00 3.63e-01 2.97e+01 angle pdb=" C ILE A 382 " pdb=" CA ILE A 382 " pdb=" CB ILE A 382 " ideal model delta sigma weight residual 112.22 104.81 7.41 1.38e+00 5.25e-01 2.89e+01 angle pdb=" N ASP R 81 " pdb=" CA ASP R 81 " pdb=" C ASP R 81 " ideal model delta sigma weight residual 113.28 121.69 -8.41 1.57e+00 4.06e-01 2.87e+01 ... (remaining 11545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 4499 15.47 - 30.95: 351 30.95 - 46.42: 77 46.42 - 61.90: 12 61.90 - 77.37: 7 Dihedral angle restraints: 4946 sinusoidal: 1680 harmonic: 3266 Sorted by residual: dihedral pdb=" C GLN A 384 " pdb=" N GLN A 384 " pdb=" CA GLN A 384 " pdb=" CB GLN A 384 " ideal model delta harmonic sigma weight residual -122.60 -110.74 -11.86 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CA ASP R 81 " pdb=" CB ASP R 81 " ideal model delta harmonic sigma weight residual 122.80 134.58 -11.78 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA LEU R 192 " pdb=" C LEU R 192 " pdb=" N LEU R 193 " pdb=" CA LEU R 193 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1225 0.097 - 0.194: 85 0.194 - 0.291: 5 0.291 - 0.388: 4 0.388 - 0.485: 4 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA ARG A 385 " pdb=" N ARG A 385 " pdb=" C ARG A 385 " pdb=" CB ARG A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" CA ASP R 81 " pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CB ASP R 81 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 1320 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 230 " -0.061 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO R 231 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO R 231 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 231 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG S 180 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO S 181 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO S 181 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO S 181 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 32 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C LYS A 32 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 32 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 33 " -0.015 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 184 2.68 - 3.23: 7893 3.23 - 3.79: 12926 3.79 - 4.34: 16840 4.34 - 4.90: 28984 Nonbonded interactions: 66827 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.165 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.191 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.199 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OD1 ASP B 186 " model vdw 2.259 3.120 ... (remaining 66822 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: 1.940 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.850 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.009 0.096 8473 Z= 0.511 Angle : 0.799 9.388 11554 Z= 0.460 Chirality : 0.058 0.485 1323 Planarity : 0.006 0.091 1483 Dihedral : 12.395 77.369 2840 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.62 % Allowed : 0.87 % Favored : 98.50 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 7.50 % 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: -0.35 (0.25), residues: 1111 helix: 1.01 (0.27), residues: 382 sheet: -0.51 (0.31), residues: 269 loop : -1.05 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 385 TYR 0.020 0.002 TYR A 263 PHE 0.026 0.002 PHE S 68 TRP 0.014 0.002 TRP B 63 HIS 0.009 0.002 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00915 ( 8471) covalent geometry : angle 0.79893 (11550) SS BOND : bond 0.00188 ( 2) SS BOND : angle 1.38043 ( 4) hydrogen bonds : bond 0.19138 ( 438) hydrogen bonds : angle 6.92190 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.478 Fit side-chains REVERT: A 14 GLU cc_start: 0.7097 (tt0) cc_final: 0.6860 (tt0) REVERT: A 381 ASP cc_start: 0.8220 (t0) cc_final: 0.7923 (t0) REVERT: A 386 MET cc_start: 0.7395 (ttm) cc_final: 0.7164 (ttm) REVERT: B 33 ILE cc_start: 0.8200 (tt) cc_final: 0.7871 (mt) REVERT: B 177 THR cc_start: 0.8402 (m) cc_final: 0.8123 (p) REVERT: B 188 MET cc_start: 0.8683 (mmm) cc_final: 0.8330 (mmm) REVERT: B 308 LEU cc_start: 0.7854 (mp) cc_final: 0.7515 (mp) REVERT: S 82 GLN cc_start: 0.8551 (tp40) cc_final: 0.8198 (tm-30) REVERT: S 183 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7268 (mp10) outliers start: 5 outliers final: 2 residues processed: 173 average time/residue: 0.5812 time to fit residues: 107.1973 Evaluate side-chains 145 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain S residue 181 PRO Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 88 ASN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105023 restraints weight = 12588.593| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.74 r_work: 0.3228 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8473 Z= 0.175 Angle : 0.643 8.587 11554 Z= 0.333 Chirality : 0.044 0.146 1323 Planarity : 0.005 0.060 1483 Dihedral : 5.073 52.812 1225 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.37 % Allowed : 10.49 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.25), residues: 1111 helix: 1.60 (0.27), residues: 377 sheet: -0.38 (0.31), residues: 267 loop : -0.92 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 18 TYR 0.019 0.002 TYR S 190 PHE 0.022 0.002 PHE S 68 TRP 0.020 0.002 TRP B 169 HIS 0.006 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8471) covalent geometry : angle 0.64287 (11550) SS BOND : bond 0.00216 ( 2) SS BOND : angle 1.55755 ( 4) hydrogen bonds : bond 0.04509 ( 438) hydrogen bonds : angle 5.02190 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.330 Fit side-chains REVERT: A 33 ASP cc_start: 0.8049 (m-30) cc_final: 0.7770 (m-30) REVERT: A 40 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 219 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6896 (tm-30) REVERT: A 381 ASP cc_start: 0.8253 (t0) cc_final: 0.7934 (t70) REVERT: B 17 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 188 MET cc_start: 0.8942 (mmm) cc_final: 0.8512 (mmm) REVERT: G 38 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7519 (ttm) REVERT: R 83 TRP cc_start: 0.5255 (t-100) cc_final: 0.4221 (t-100) REVERT: S 82 GLN cc_start: 0.8718 (tp40) cc_final: 0.8490 (mm-40) outliers start: 19 outliers final: 7 residues processed: 156 average time/residue: 0.6689 time to fit residues: 110.3461 Evaluate side-chains 148 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 26 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 77 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 239 ASN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101341 restraints weight = 12689.884| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.76 r_work: 0.3217 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8473 Z= 0.143 Angle : 0.583 8.639 11554 Z= 0.301 Chirality : 0.042 0.135 1323 Planarity : 0.005 0.053 1483 Dihedral : 4.850 55.231 1222 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.62 % Allowed : 14.11 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.35 (0.25), residues: 1111 helix: 1.90 (0.27), residues: 377 sheet: -0.22 (0.32), residues: 257 loop : -0.84 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 225 TYR 0.019 0.001 TYR R 275 PHE 0.014 0.001 PHE A 222 TRP 0.016 0.001 TRP B 169 HIS 0.009 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8471) covalent geometry : angle 0.58294 (11550) SS BOND : bond 0.00249 ( 2) SS BOND : angle 1.24051 ( 4) hydrogen bonds : bond 0.04128 ( 438) hydrogen bonds : angle 4.71944 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.326 Fit side-chains REVERT: A 33 ASP cc_start: 0.8089 (m-30) cc_final: 0.7827 (m-30) REVERT: A 219 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6915 (tm-30) REVERT: A 381 ASP cc_start: 0.8307 (t0) cc_final: 0.7990 (t70) REVERT: B 17 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7781 (tt0) REVERT: B 33 ILE cc_start: 0.8166 (tt) cc_final: 0.7846 (mt) REVERT: B 188 MET cc_start: 0.8897 (mmm) cc_final: 0.8509 (mmm) REVERT: B 217 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7869 (pmt) REVERT: B 223 THR cc_start: 0.8131 (p) cc_final: 0.7902 (p) REVERT: R 83 TRP cc_start: 0.5283 (t-100) cc_final: 0.4875 (t-100) REVERT: S 5 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.8035 (t) REVERT: S 183 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7409 (mm-40) outliers start: 21 outliers final: 8 residues processed: 156 average time/residue: 0.6615 time to fit residues: 109.1853 Evaluate side-chains 150 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 35 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 239 ASN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101026 restraints weight = 12917.148| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.77 r_work: 0.3214 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8473 Z= 0.141 Angle : 0.579 8.641 11554 Z= 0.297 Chirality : 0.042 0.133 1323 Planarity : 0.005 0.054 1483 Dihedral : 4.760 54.641 1222 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.75 % Allowed : 16.35 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.25), residues: 1111 helix: 1.99 (0.27), residues: 378 sheet: -0.20 (0.32), residues: 252 loop : -0.77 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.020 0.001 TYR R 275 PHE 0.014 0.001 PHE R 107 TRP 0.015 0.001 TRP B 169 HIS 0.009 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8471) covalent geometry : angle 0.57852 (11550) SS BOND : bond 0.00254 ( 2) SS BOND : angle 1.17416 ( 4) hydrogen bonds : bond 0.03927 ( 438) hydrogen bonds : angle 4.62162 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.370 Fit side-chains REVERT: A 33 ASP cc_start: 0.8072 (m-30) cc_final: 0.7850 (m-30) REVERT: A 38 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7243 (mtt90) REVERT: A 219 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6882 (tm-30) REVERT: A 381 ASP cc_start: 0.8300 (t0) cc_final: 0.7986 (t70) REVERT: B 17 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7787 (tt0) REVERT: B 33 ILE cc_start: 0.8192 (tt) cc_final: 0.7906 (mt) REVERT: B 188 MET cc_start: 0.8878 (mmm) cc_final: 0.8478 (mmm) REVERT: B 223 THR cc_start: 0.8124 (p) cc_final: 0.7892 (p) REVERT: S 5 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8060 (t) REVERT: S 80 PHE cc_start: 0.8635 (m-80) cc_final: 0.8346 (m-80) REVERT: S 183 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7376 (mm-40) outliers start: 22 outliers final: 11 residues processed: 151 average time/residue: 0.6599 time to fit residues: 105.4123 Evaluate side-chains 154 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098467 restraints weight = 12919.091| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.77 r_work: 0.3172 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8473 Z= 0.211 Angle : 0.637 8.979 11554 Z= 0.325 Chirality : 0.044 0.133 1323 Planarity : 0.005 0.054 1483 Dihedral : 5.038 54.805 1222 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.12 % Allowed : 16.85 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.32 (0.25), residues: 1111 helix: 1.79 (0.26), residues: 383 sheet: -0.14 (0.32), residues: 261 loop : -0.88 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 27 TYR 0.019 0.002 TYR B 85 PHE 0.017 0.002 PHE R 107 TRP 0.016 0.002 TRP B 169 HIS 0.009 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 8471) covalent geometry : angle 0.63650 (11550) SS BOND : bond 0.00136 ( 2) SS BOND : angle 1.44262 ( 4) hydrogen bonds : bond 0.04423 ( 438) hydrogen bonds : angle 4.74173 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.341 Fit side-chains REVERT: A 38 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7218 (mtt90) REVERT: A 40 THR cc_start: 0.8916 (t) cc_final: 0.8561 (m) REVERT: A 381 ASP cc_start: 0.8297 (t0) cc_final: 0.7980 (t70) REVERT: B 17 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7835 (tt0) REVERT: B 29 THR cc_start: 0.8035 (t) cc_final: 0.7781 (p) REVERT: B 33 ILE cc_start: 0.8239 (tt) cc_final: 0.7943 (mt) REVERT: B 188 MET cc_start: 0.8877 (mmm) cc_final: 0.8487 (mmm) REVERT: S 5 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8039 (t) REVERT: S 80 PHE cc_start: 0.8726 (m-80) cc_final: 0.8413 (m-80) REVERT: S 180 ARG cc_start: 0.7340 (mtt90) cc_final: 0.7014 (mtt180) REVERT: S 183 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7498 (mm-40) outliers start: 25 outliers final: 12 residues processed: 159 average time/residue: 0.6868 time to fit residues: 115.3042 Evaluate side-chains 159 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.0170 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100704 restraints weight = 12710.878| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.75 r_work: 0.3206 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8473 Z= 0.137 Angle : 0.580 8.661 11554 Z= 0.295 Chirality : 0.042 0.129 1323 Planarity : 0.004 0.051 1483 Dihedral : 4.807 56.064 1222 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.87 % Allowed : 19.23 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1111 helix: 2.03 (0.27), residues: 383 sheet: -0.17 (0.32), residues: 261 loop : -0.83 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 225 TYR 0.022 0.001 TYR R 275 PHE 0.013 0.001 PHE A 222 TRP 0.017 0.001 TRP B 169 HIS 0.012 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8471) covalent geometry : angle 0.58001 (11550) SS BOND : bond 0.00275 ( 2) SS BOND : angle 1.11357 ( 4) hydrogen bonds : bond 0.03849 ( 438) hydrogen bonds : angle 4.55593 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.287 Fit side-chains REVERT: A 35 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7585 (mm110) REVERT: A 38 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7255 (mtt90) REVERT: A 219 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7113 (tt0) REVERT: A 368 ASP cc_start: 0.7405 (m-30) cc_final: 0.7121 (t0) REVERT: A 381 ASP cc_start: 0.8267 (t0) cc_final: 0.7972 (t70) REVERT: B 17 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7856 (tt0) REVERT: B 29 THR cc_start: 0.7976 (t) cc_final: 0.7747 (p) REVERT: B 33 ILE cc_start: 0.8225 (tt) cc_final: 0.7924 (mt) REVERT: B 188 MET cc_start: 0.8858 (mmm) cc_final: 0.8467 (mmm) REVERT: B 217 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8091 (pmt) REVERT: R 83 TRP cc_start: 0.5306 (t-100) cc_final: 0.4657 (t-100) REVERT: S 5 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.8025 (t) REVERT: S 183 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7377 (mm-40) outliers start: 23 outliers final: 12 residues processed: 151 average time/residue: 0.6761 time to fit residues: 107.7929 Evaluate side-chains 156 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.0030 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS S 39 GLN S 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098850 restraints weight = 12880.764| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.68 r_work: 0.3194 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8473 Z= 0.190 Angle : 0.625 8.416 11554 Z= 0.318 Chirality : 0.044 0.133 1323 Planarity : 0.005 0.051 1483 Dihedral : 5.004 55.701 1222 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.87 % Allowed : 20.10 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.37 (0.25), residues: 1111 helix: 1.89 (0.26), residues: 384 sheet: -0.21 (0.32), residues: 261 loop : -0.84 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 225 TYR 0.021 0.002 TYR R 275 PHE 0.015 0.002 PHE R 107 TRP 0.016 0.002 TRP B 169 HIS 0.013 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 8471) covalent geometry : angle 0.62491 (11550) SS BOND : bond 0.00179 ( 2) SS BOND : angle 1.32082 ( 4) hydrogen bonds : bond 0.04235 ( 438) hydrogen bonds : angle 4.64448 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.295 Fit side-chains REVERT: A 38 ARG cc_start: 0.7617 (mtm110) cc_final: 0.7250 (mtt90) REVERT: A 40 THR cc_start: 0.8889 (t) cc_final: 0.8501 (m) REVERT: A 219 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7185 (tt0) REVERT: A 368 ASP cc_start: 0.7491 (m-30) cc_final: 0.7184 (t0) REVERT: A 381 ASP cc_start: 0.8260 (t0) cc_final: 0.7977 (t70) REVERT: B 17 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7872 (tt0) REVERT: B 29 THR cc_start: 0.8009 (t) cc_final: 0.7760 (p) REVERT: B 33 ILE cc_start: 0.8220 (tt) cc_final: 0.7907 (mt) REVERT: B 188 MET cc_start: 0.8849 (mmm) cc_final: 0.8463 (mmm) REVERT: R 126 PRO cc_start: 0.7808 (Cg_endo) cc_final: 0.7528 (Cg_exo) REVERT: S 5 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.8023 (t) REVERT: S 180 ARG cc_start: 0.7303 (mtt90) cc_final: 0.6964 (mtt180) REVERT: S 183 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7477 (mm-40) outliers start: 23 outliers final: 15 residues processed: 154 average time/residue: 0.7133 time to fit residues: 115.7640 Evaluate side-chains 160 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 75 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099259 restraints weight = 12728.850| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.68 r_work: 0.3202 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8473 Z= 0.177 Angle : 0.618 8.807 11554 Z= 0.313 Chirality : 0.043 0.130 1323 Planarity : 0.005 0.053 1483 Dihedral : 5.009 57.056 1222 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.12 % Allowed : 20.22 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.31 (0.25), residues: 1111 helix: 1.84 (0.26), residues: 389 sheet: -0.23 (0.32), residues: 261 loop : -0.92 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 27 TYR 0.024 0.002 TYR B 85 PHE 0.014 0.002 PHE R 107 TRP 0.017 0.002 TRP B 169 HIS 0.011 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8471) covalent geometry : angle 0.61784 (11550) SS BOND : bond 0.00202 ( 2) SS BOND : angle 1.23202 ( 4) hydrogen bonds : bond 0.04084 ( 438) hydrogen bonds : angle 4.62042 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7222 (mtt90) REVERT: A 40 THR cc_start: 0.8888 (t) cc_final: 0.8503 (m) REVERT: A 219 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7167 (tt0) REVERT: A 368 ASP cc_start: 0.7432 (m-30) cc_final: 0.7103 (t0) REVERT: A 381 ASP cc_start: 0.8261 (t0) cc_final: 0.7981 (t70) REVERT: B 17 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7886 (tt0) REVERT: B 33 ILE cc_start: 0.8203 (tt) cc_final: 0.7908 (mt) REVERT: B 188 MET cc_start: 0.8834 (mmm) cc_final: 0.8457 (mmm) REVERT: B 217 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7799 (pmt) REVERT: S 180 ARG cc_start: 0.7308 (mtt90) cc_final: 0.6979 (mtt180) REVERT: S 183 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7524 (mm-40) outliers start: 25 outliers final: 15 residues processed: 154 average time/residue: 0.6969 time to fit residues: 113.1940 Evaluate side-chains 154 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099079 restraints weight = 12748.474| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.75 r_work: 0.3194 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8473 Z= 0.170 Angle : 0.615 8.625 11554 Z= 0.311 Chirality : 0.043 0.133 1323 Planarity : 0.005 0.053 1483 Dihedral : 5.014 57.500 1222 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.50 % Allowed : 21.10 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.38 (0.25), residues: 1111 helix: 1.96 (0.27), residues: 383 sheet: -0.22 (0.32), residues: 260 loop : -0.90 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 27 TYR 0.023 0.002 TYR R 275 PHE 0.014 0.002 PHE R 107 TRP 0.017 0.002 TRP B 169 HIS 0.011 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8471) covalent geometry : angle 0.61503 (11550) SS BOND : bond 0.00253 ( 2) SS BOND : angle 1.15944 ( 4) hydrogen bonds : bond 0.04047 ( 438) hydrogen bonds : angle 4.61292 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.312 Fit side-chains REVERT: A 38 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7242 (mtt90) REVERT: A 40 THR cc_start: 0.8880 (t) cc_final: 0.8531 (m) REVERT: A 219 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7174 (tt0) REVERT: A 381 ASP cc_start: 0.8260 (t0) cc_final: 0.7982 (t70) REVERT: B 17 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7904 (tt0) REVERT: B 33 ILE cc_start: 0.8220 (tt) cc_final: 0.7939 (mt) REVERT: B 188 MET cc_start: 0.8832 (mmm) cc_final: 0.8444 (mmm) REVERT: B 217 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7892 (pmt) REVERT: S 180 ARG cc_start: 0.7322 (mtt90) cc_final: 0.7008 (mtt180) REVERT: S 183 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7539 (mm-40) outliers start: 20 outliers final: 16 residues processed: 147 average time/residue: 0.6842 time to fit residues: 106.0636 Evaluate side-chains 155 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 0.0030 chunk 63 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.0050 chunk 95 optimal weight: 0.6980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100606 restraints weight = 12724.656| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.67 r_work: 0.3223 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8473 Z= 0.141 Angle : 0.593 8.432 11554 Z= 0.300 Chirality : 0.042 0.152 1323 Planarity : 0.005 0.050 1483 Dihedral : 4.904 58.664 1222 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.12 % Allowed : 21.35 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.46 (0.25), residues: 1111 helix: 2.09 (0.27), residues: 383 sheet: -0.26 (0.32), residues: 261 loop : -0.86 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 27 TYR 0.024 0.001 TYR R 275 PHE 0.013 0.001 PHE R 107 TRP 0.018 0.002 TRP B 169 HIS 0.010 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8471) covalent geometry : angle 0.59237 (11550) SS BOND : bond 0.00237 ( 2) SS BOND : angle 1.06056 ( 4) hydrogen bonds : bond 0.03793 ( 438) hydrogen bonds : angle 4.51469 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.250 Fit side-chains REVERT: A 38 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7183 (mtt90) REVERT: A 40 THR cc_start: 0.8784 (t) cc_final: 0.8468 (m) REVERT: A 381 ASP cc_start: 0.8262 (t0) cc_final: 0.7981 (t70) REVERT: B 33 ILE cc_start: 0.8194 (tt) cc_final: 0.7922 (mt) REVERT: B 137 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7695 (ttm110) REVERT: B 188 MET cc_start: 0.8791 (mmm) cc_final: 0.8403 (mmm) REVERT: R 46 VAL cc_start: 0.6924 (t) cc_final: 0.6687 (p) REVERT: S 23 SER cc_start: 0.8732 (t) cc_final: 0.8459 (p) REVERT: S 180 ARG cc_start: 0.7288 (mtt90) cc_final: 0.6994 (mtt180) REVERT: S 183 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7494 (mm-40) outliers start: 17 outliers final: 13 residues processed: 149 average time/residue: 0.6672 time to fit residues: 104.7732 Evaluate side-chains 149 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 68 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.101293 restraints weight = 12774.032| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.80 r_work: 0.3205 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8473 Z= 0.155 Angle : 0.608 8.496 11554 Z= 0.307 Chirality : 0.042 0.161 1323 Planarity : 0.005 0.050 1483 Dihedral : 4.952 59.771 1222 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.25 % Allowed : 21.47 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1111 helix: 2.08 (0.27), residues: 383 sheet: -0.26 (0.32), residues: 261 loop : -0.87 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 27 TYR 0.022 0.002 TYR R 275 PHE 0.013 0.002 PHE R 107 TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8471) covalent geometry : angle 0.60745 (11550) SS BOND : bond 0.00218 ( 2) SS BOND : angle 1.09458 ( 4) hydrogen bonds : bond 0.03909 ( 438) hydrogen bonds : angle 4.53790 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3317.70 seconds wall clock time: 57 minutes 23.34 seconds (3443.34 seconds total)