Starting phenix.real_space_refine on Wed Feb 12 06:31:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hti_35010/02_2025/8hti_35010_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hti_35010/02_2025/8hti_35010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hti_35010/02_2025/8hti_35010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hti_35010/02_2025/8hti_35010.map" model { file = "/net/cci-nas-00/data/ceres_data/8hti_35010/02_2025/8hti_35010_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hti_35010/02_2025/8hti_35010_neut.cif" } resolution = 2.97 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= 0.024 sd= 0.080 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 51 5.16 5 C 4757 2.51 5 N 1274 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7390 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1311 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain breaks: 4 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2454 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 49 Chain: "G" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 364 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 848 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 285} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 OCA R 401 " occ=0.00 ... (8 atoms not shown) pdb=" O2 OCA R 401 " occ=0.00 Time building chain proxies: 5.22, per 1000 atoms: 0.71 Number of scatterers: 7390 At special positions: 0 Unit cell: (82.547, 95.312, 133.607, 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 51 16.00 O 1308 8.00 N 1274 7.00 C 4757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 99 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 171 " - pdb=" SG CYS R 191 " 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: 1.78 Conformation dependent library (CDL) restraints added in 996.3 milliseconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 11 sheets defined 39.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.539A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.739A pdb=" N CYS A 223 " --> pdb=" O TRP A 220 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 225 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.590A pdb=" N ILE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 377 Processing helix chain 'B' and resid 10 through 26 removed outlier: 3.612A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.587A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 30 through 44 removed outlier: 3.558A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.744A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 26 removed outlier: 3.882A pdb=" N HIS R 26 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 54 removed outlier: 4.285A pdb=" N PHE R 33 " --> pdb=" O ILE R 29 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 78 removed outlier: 3.530A pdb=" N THR R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 Processing helix chain 'R' and resid 96 through 130 Processing helix chain 'R' and resid 133 through 138 Processing helix chain 'R' and resid 139 through 159 Processing helix chain 'R' and resid 159 through 166 removed outlier: 4.567A pdb=" N PHE R 163 " --> pdb=" O ILE R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 188 removed outlier: 3.771A pdb=" N VAL R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 228 removed outlier: 3.607A pdb=" N GLY R 210 " --> pdb=" O LEU R 206 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 267 removed outlier: 4.233A pdb=" N LYS R 238 " --> pdb=" O ASP R 234 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER R 245 " --> pdb=" O SER R 241 " (cutoff:3.500A) Proline residue: R 256 - end of helix removed outlier: 4.397A pdb=" N ARG R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY R 267 " --> pdb=" O THR R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 280 removed outlier: 3.670A pdb=" N HIS R 275 " --> pdb=" O PRO R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 295 removed outlier: 3.596A pdb=" N MET R 288 " --> pdb=" O LEU R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'R' and resid 298 through 310 removed outlier: 3.739A pdb=" N ARG R 302 " --> pdb=" O THR R 298 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU R 303 " --> pdb=" O LYS R 299 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG R 304 " --> pdb=" O GLN R 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE R 309 " --> pdb=" O VAL R 305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199 removed outlier: 3.588A pdb=" N PHE A 208 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N ALA A 229 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG A 42 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE A 231 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 44 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL A 233 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU A 46 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 230 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE A 276 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE A 232 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.858A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.756A 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 62 removed outlier: 7.080A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.153A 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: 6.742A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.842A 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: 6.783A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.833A 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: 7.205A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.475A 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: 6.786A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.543A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.573A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 93 through 95 removed outlier: 8.244A pdb=" N ILE R 176 " --> pdb=" O SER R 13 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU R 15 " --> pdb=" O ILE R 176 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1008 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: 1.98 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2367 1.34 - 1.46: 1821 1.46 - 1.58: 3291 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 7551 Sorted by residual: bond pdb=" N ASP B 312 " pdb=" CA ASP B 312 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.35e-02 5.49e+03 6.24e+00 bond pdb=" N HIS R 183 " pdb=" CA HIS R 183 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.24e-02 6.50e+03 5.42e+00 bond pdb=" CE1 HIS R 183 " pdb=" NE2 HIS R 183 " ideal model delta sigma weight residual 1.321 1.338 -0.017 1.00e-02 1.00e+04 2.86e+00 bond pdb=" C HIS R 183 " pdb=" O HIS R 183 " ideal model delta sigma weight residual 1.236 1.247 -0.012 1.19e-02 7.06e+03 9.35e-01 bond pdb=" CA ILE R 159 " pdb=" C ILE R 159 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.05e-02 9.07e+03 8.68e-01 ... (remaining 7546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 9911 1.45 - 2.90: 294 2.90 - 4.35: 32 4.35 - 5.81: 10 5.81 - 7.26: 5 Bond angle restraints: 10252 Sorted by residual: angle pdb=" N ILE R 159 " pdb=" CA ILE R 159 " pdb=" C ILE R 159 " ideal model delta sigma weight residual 108.88 114.86 -5.98 2.16e+00 2.14e-01 7.66e+00 angle pdb=" C HIS R 10 " pdb=" N PRO R 11 " pdb=" CA PRO R 11 " ideal model delta sigma weight residual 120.03 122.72 -2.69 9.90e-01 1.02e+00 7.38e+00 angle pdb=" N ASP B 312 " pdb=" CA ASP B 312 " pdb=" C ASP B 312 " ideal model delta sigma weight residual 113.38 110.28 3.10 1.23e+00 6.61e-01 6.34e+00 angle pdb=" N GLY B 306 " pdb=" CA GLY B 306 " pdb=" C GLY B 306 " ideal model delta sigma weight residual 110.38 114.03 -3.65 1.48e+00 4.57e-01 6.09e+00 angle pdb=" CA HIS R 183 " pdb=" C HIS R 183 " pdb=" O HIS R 183 " ideal model delta sigma weight residual 120.55 117.99 2.56 1.07e+00 8.73e-01 5.73e+00 ... (remaining 10247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 3913 17.74 - 35.49: 418 35.49 - 53.23: 96 53.23 - 70.98: 18 70.98 - 88.72: 7 Dihedral angle restraints: 4452 sinusoidal: 1657 harmonic: 2795 Sorted by residual: dihedral pdb=" CB CYS R 171 " pdb=" SG CYS R 171 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -134.25 48.25 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP R 123 " pdb=" CB ASP R 123 " pdb=" CG ASP R 123 " pdb=" OD1 ASP R 123 " ideal model delta sinusoidal sigma weight residual -30.00 -89.16 59.16 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 4449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 774 0.036 - 0.073: 309 0.073 - 0.109: 76 0.109 - 0.146: 28 0.146 - 0.182: 1 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CB ILE R 159 " pdb=" CA ILE R 159 " pdb=" CG1 ILE R 159 " pdb=" CG2 ILE R 159 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA PHE R 109 " pdb=" N PHE R 109 " pdb=" C PHE R 109 " pdb=" CB PHE R 109 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1185 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 159 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO R 160 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO R 160 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 160 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 286 " 0.042 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO R 287 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO R 287 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 287 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO B 236 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.031 5.00e-02 4.00e+02 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1874 2.80 - 3.33: 6272 3.33 - 3.85: 11515 3.85 - 4.38: 13093 4.38 - 4.90: 24242 Nonbonded interactions: 56996 Sorted by model distance: nonbonded pdb=" O ASN N 77 " pdb=" OD1 ASN N 77 " model vdw 2.277 3.040 nonbonded pdb=" OG SER R 114 " pdb=" OD2 ASP R 212 " model vdw 2.305 3.040 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.306 3.120 nonbonded pdb=" O ILE R 276 " pdb=" ND2 ASN R 280 " model vdw 2.322 3.120 nonbonded pdb=" O SER R 8 " pdb=" OG SER R 8 " model vdw 2.342 3.040 ... (remaining 56991 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=0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.580 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.190 Find NCS groups from input model: 0.080 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 0.045 7551 Z= 0.234 Angle : 0.603 7.257 10252 Z= 0.341 Chirality : 0.043 0.182 1188 Planarity : 0.005 0.064 1288 Dihedral : 15.486 88.721 2633 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 17.04 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.28), residues: 940 helix: 1.81 (0.30), residues: 345 sheet: 0.26 (0.37), residues: 201 loop : -1.35 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 339 HIS 0.006 0.001 HIS R 178 PHE 0.021 0.001 PHE A 259 TYR 0.016 0.002 TYR N 117 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.810 Fit side-chains REVERT: B 294 CYS cc_start: 0.8392 (p) cc_final: 0.8171 (m) REVERT: G 19 LEU cc_start: 0.8130 (mt) cc_final: 0.7906 (mm) REVERT: R 9 PHE cc_start: 0.8071 (t80) cc_final: 0.7786 (t80) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 1.3392 time to fit residues: 150.8850 Evaluate side-chains 91 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS A 376 GLN R 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.111988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.094951 restraints weight = 12236.082| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.97 r_work: 0.3206 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7551 Z= 0.202 Angle : 0.545 7.071 10252 Z= 0.286 Chirality : 0.043 0.142 1188 Planarity : 0.005 0.061 1288 Dihedral : 4.149 28.939 1042 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.01 % Allowed : 18.87 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.28), residues: 940 helix: 2.14 (0.30), residues: 342 sheet: 0.33 (0.38), residues: 200 loop : -1.18 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 220 HIS 0.005 0.001 HIS R 178 PHE 0.016 0.001 PHE R 109 TYR 0.011 0.001 TYR N 117 ARG 0.008 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.853 Fit side-chains REVERT: A 29 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8408 (tp-100) REVERT: B 96 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7119 (ttt-90) REVERT: B 101 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8433 (ptm) REVERT: B 294 CYS cc_start: 0.8529 (p) cc_final: 0.8116 (p) REVERT: R 93 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: R 304 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.5960 (mpp80) outliers start: 23 outliers final: 7 residues processed: 111 average time/residue: 1.2401 time to fit residues: 145.6973 Evaluate side-chains 104 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 93 GLU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 0.0770 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.113792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096830 restraints weight = 12400.887| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.99 r_work: 0.3240 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 7551 Z= 0.138 Angle : 0.490 6.886 10252 Z= 0.255 Chirality : 0.041 0.134 1188 Planarity : 0.004 0.057 1288 Dihedral : 3.894 28.262 1042 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.54 % Allowed : 19.27 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.28), residues: 940 helix: 2.47 (0.30), residues: 341 sheet: 0.33 (0.37), residues: 211 loop : -1.19 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS R 178 PHE 0.014 0.001 PHE R 109 TYR 0.009 0.001 TYR R 134 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.835 Fit side-chains REVERT: A 29 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8435 (tp-100) REVERT: B 52 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7675 (ptp90) REVERT: B 96 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7084 (ttt-90) REVERT: B 101 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8451 (ptm) REVERT: B 136 SER cc_start: 0.8562 (t) cc_final: 0.8361 (m) REVERT: B 294 CYS cc_start: 0.8488 (p) cc_final: 0.8058 (p) REVERT: R 304 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.5820 (mpp80) REVERT: R 307 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7484 (ttmm) outliers start: 27 outliers final: 7 residues processed: 116 average time/residue: 1.1817 time to fit residues: 145.2901 Evaluate side-chains 108 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 179 THR Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.0030 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.096581 restraints weight = 12237.086| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.95 r_work: 0.3236 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7551 Z= 0.156 Angle : 0.499 6.880 10252 Z= 0.259 Chirality : 0.041 0.131 1188 Planarity : 0.004 0.057 1288 Dihedral : 3.893 27.364 1042 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.62 % Allowed : 21.76 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.28), residues: 940 helix: 2.51 (0.30), residues: 343 sheet: 0.49 (0.37), residues: 211 loop : -1.23 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS R 178 PHE 0.020 0.001 PHE R 89 TYR 0.010 0.001 TYR A 344 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.708 Fit side-chains REVERT: A 29 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8419 (tp-100) REVERT: A 371 ARG cc_start: 0.8364 (mtt90) cc_final: 0.7970 (mtp-110) REVERT: B 52 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7643 (ptp90) REVERT: B 96 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7089 (ttt-90) REVERT: B 101 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8458 (ptm) REVERT: B 294 CYS cc_start: 0.8467 (p) cc_final: 0.8027 (p) REVERT: R 26 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7627 (m170) REVERT: R 304 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.5688 (mpp80) REVERT: R 307 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7471 (ttmm) outliers start: 20 outliers final: 8 residues processed: 111 average time/residue: 1.2378 time to fit residues: 145.2612 Evaluate side-chains 109 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.095941 restraints weight = 12309.628| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.94 r_work: 0.3227 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7551 Z= 0.178 Angle : 0.505 7.055 10252 Z= 0.264 Chirality : 0.042 0.132 1188 Planarity : 0.004 0.056 1288 Dihedral : 3.954 27.296 1042 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.15 % Allowed : 20.97 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.28), residues: 940 helix: 2.49 (0.29), residues: 347 sheet: 0.48 (0.36), residues: 210 loop : -1.21 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS R 178 PHE 0.015 0.001 PHE R 109 TYR 0.011 0.001 TYR A 344 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.833 Fit side-chains REVERT: A 29 GLN cc_start: 0.8817 (tp-100) cc_final: 0.8457 (tp-100) REVERT: A 371 ARG cc_start: 0.8362 (mtt90) cc_final: 0.7988 (mtp-110) REVERT: B 52 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7639 (ptp90) REVERT: B 96 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7051 (ttt-90) REVERT: B 101 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8444 (ptm) REVERT: B 294 CYS cc_start: 0.8474 (p) cc_final: 0.8052 (p) REVERT: G 19 LEU cc_start: 0.7849 (mt) cc_final: 0.7623 (mm) REVERT: R 26 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.7656 (m170) REVERT: R 304 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.5762 (mpp80) REVERT: R 307 LYS cc_start: 0.7733 (ttmt) cc_final: 0.7407 (ttmm) outliers start: 24 outliers final: 10 residues processed: 113 average time/residue: 1.2826 time to fit residues: 153.1379 Evaluate side-chains 110 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093992 restraints weight = 12303.757| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.95 r_work: 0.3193 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7551 Z= 0.236 Angle : 0.549 7.436 10252 Z= 0.288 Chirality : 0.043 0.147 1188 Planarity : 0.004 0.057 1288 Dihedral : 4.215 30.351 1042 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.28 % Allowed : 20.84 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.28), residues: 940 helix: 2.31 (0.29), residues: 347 sheet: 0.63 (0.37), residues: 200 loop : -1.24 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 63 HIS 0.005 0.001 HIS R 275 PHE 0.016 0.001 PHE R 109 TYR 0.012 0.001 TYR R 134 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.772 Fit side-chains REVERT: A 29 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8418 (tp-100) REVERT: A 371 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7969 (mtm110) REVERT: B 52 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7615 (ptp90) REVERT: B 96 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7092 (ttt-90) REVERT: B 101 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8509 (ptm) REVERT: B 251 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7963 (mtt-85) REVERT: B 294 CYS cc_start: 0.8538 (p) cc_final: 0.8073 (p) REVERT: R 26 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7684 (m170) REVERT: R 304 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.5785 (mpp80) REVERT: R 307 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7400 (ttmm) outliers start: 25 outliers final: 12 residues processed: 114 average time/residue: 1.2089 time to fit residues: 145.9016 Evaluate side-chains 115 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.0020 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094814 restraints weight = 12364.024| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.02 r_work: 0.3204 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7551 Z= 0.182 Angle : 0.512 7.191 10252 Z= 0.269 Chirality : 0.042 0.133 1188 Planarity : 0.004 0.056 1288 Dihedral : 4.120 30.910 1042 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.54 % Allowed : 21.49 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.28), residues: 940 helix: 2.47 (0.29), residues: 346 sheet: 0.42 (0.36), residues: 210 loop : -1.18 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.004 0.001 HIS R 275 PHE 0.015 0.001 PHE R 109 TYR 0.013 0.001 TYR A 344 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.849 Fit side-chains REVERT: A 29 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8460 (tp-100) REVERT: A 34 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8497 (ttpp) REVERT: A 371 ARG cc_start: 0.8339 (mtt90) cc_final: 0.7959 (mtm110) REVERT: B 52 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7651 (ptp90) REVERT: B 96 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7102 (ttt-90) REVERT: B 101 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8474 (ptm) REVERT: B 251 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7961 (mtt-85) REVERT: B 294 CYS cc_start: 0.8518 (p) cc_final: 0.8224 (m) REVERT: R 26 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7721 (m170) REVERT: R 304 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.5762 (mpp80) REVERT: R 307 LYS cc_start: 0.7712 (ttmt) cc_final: 0.7383 (ttmm) outliers start: 27 outliers final: 13 residues processed: 112 average time/residue: 1.2404 time to fit residues: 146.9299 Evaluate side-chains 116 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.112177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095424 restraints weight = 12375.853| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.96 r_work: 0.3218 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7551 Z= 0.167 Angle : 0.502 7.024 10252 Z= 0.263 Chirality : 0.042 0.132 1188 Planarity : 0.004 0.056 1288 Dihedral : 4.052 30.779 1042 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.54 % Allowed : 20.97 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.28), residues: 940 helix: 2.53 (0.29), residues: 346 sheet: 0.39 (0.36), residues: 212 loop : -1.20 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.003 0.001 HIS R 275 PHE 0.014 0.001 PHE R 109 TYR 0.010 0.001 TYR R 134 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.854 Fit side-chains REVERT: A 29 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8445 (tp-100) REVERT: A 34 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8506 (ttpp) REVERT: A 371 ARG cc_start: 0.8365 (mtt90) cc_final: 0.7959 (mtm110) REVERT: B 52 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7643 (ptp90) REVERT: B 96 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7069 (ttt-90) REVERT: B 101 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8458 (ptm) REVERT: B 156 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8592 (mt0) REVERT: B 251 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8070 (mtt-85) REVERT: B 294 CYS cc_start: 0.8512 (p) cc_final: 0.8227 (m) REVERT: R 26 HIS cc_start: 0.8072 (OUTLIER) cc_final: 0.7707 (m170) REVERT: R 304 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.5740 (mpp80) REVERT: R 307 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7373 (ttmm) outliers start: 27 outliers final: 13 residues processed: 112 average time/residue: 1.2459 time to fit residues: 147.7344 Evaluate side-chains 120 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 74 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.0270 chunk 75 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.096115 restraints weight = 12452.729| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.97 r_work: 0.3229 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7551 Z= 0.155 Angle : 0.494 6.821 10252 Z= 0.260 Chirality : 0.041 0.132 1188 Planarity : 0.004 0.056 1288 Dihedral : 3.964 29.530 1042 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.15 % Allowed : 21.23 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.28), residues: 940 helix: 2.64 (0.29), residues: 345 sheet: 0.44 (0.36), residues: 212 loop : -1.16 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.003 0.001 HIS R 275 PHE 0.022 0.001 PHE R 89 TYR 0.015 0.001 TYR N 80 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.823 Fit side-chains REVERT: A 29 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8456 (tp-100) REVERT: A 371 ARG cc_start: 0.8357 (mtt90) cc_final: 0.7943 (mtm110) REVERT: B 52 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7631 (ptp90) REVERT: B 96 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7058 (ttt-90) REVERT: B 101 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8474 (ptm) REVERT: B 137 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8168 (ttm-80) REVERT: B 156 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8593 (mt0) REVERT: B 251 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8005 (mtt-85) REVERT: B 294 CYS cc_start: 0.8500 (p) cc_final: 0.8218 (m) REVERT: R 26 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7682 (m170) REVERT: R 304 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.5737 (mpp80) REVERT: R 307 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7433 (ttmm) outliers start: 24 outliers final: 14 residues processed: 114 average time/residue: 1.1868 time to fit residues: 143.4445 Evaluate side-chains 120 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.095065 restraints weight = 12484.857| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.95 r_work: 0.3212 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7551 Z= 0.204 Angle : 0.525 7.437 10252 Z= 0.275 Chirality : 0.043 0.136 1188 Planarity : 0.004 0.057 1288 Dihedral : 4.073 30.656 1042 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.01 % Allowed : 22.02 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.28), residues: 940 helix: 2.51 (0.29), residues: 345 sheet: 0.48 (0.36), residues: 210 loop : -1.24 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS R 275 PHE 0.015 0.001 PHE R 109 TYR 0.011 0.001 TYR R 134 ARG 0.006 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.835 Fit side-chains REVERT: A 29 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8447 (tp-100) REVERT: A 371 ARG cc_start: 0.8379 (mtt90) cc_final: 0.7969 (mtm110) REVERT: B 52 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7648 (ptp90) REVERT: B 96 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7080 (ttt-90) REVERT: B 101 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8422 (ptm) REVERT: B 137 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8205 (ttm-80) REVERT: B 156 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8583 (mt0) REVERT: B 251 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7945 (mtt-85) REVERT: B 294 CYS cc_start: 0.8519 (p) cc_final: 0.8245 (m) REVERT: R 26 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7703 (m170) REVERT: R 304 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.5699 (mpp80) REVERT: R 307 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7465 (ttmm) outliers start: 23 outliers final: 15 residues processed: 116 average time/residue: 1.2219 time to fit residues: 149.7963 Evaluate side-chains 120 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 68 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 62 optimal weight: 0.0570 chunk 16 optimal weight: 0.0010 overall best weight: 0.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.114695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.098150 restraints weight = 12366.282| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.95 r_work: 0.3263 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7551 Z= 0.119 Angle : 0.466 6.636 10252 Z= 0.245 Chirality : 0.040 0.131 1188 Planarity : 0.004 0.056 1288 Dihedral : 3.785 26.794 1042 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.70 % Allowed : 23.85 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.29), residues: 940 helix: 2.84 (0.30), residues: 342 sheet: 0.52 (0.36), residues: 213 loop : -1.11 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 220 HIS 0.004 0.000 HIS A 343 PHE 0.022 0.001 PHE R 89 TYR 0.012 0.001 TYR N 80 ARG 0.006 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5601.64 seconds wall clock time: 99 minutes 41.87 seconds (5981.87 seconds total)