Starting phenix.real_space_refine on Tue Sep 24 09:32:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/09_2024/7dhi_30681.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/09_2024/7dhi_30681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/09_2024/7dhi_30681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/09_2024/7dhi_30681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/09_2024/7dhi_30681.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/09_2024/7dhi_30681.cif" } resolution = 3.26 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= 0.000 sd= 0.005 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 48 5.16 5 C 4990 2.51 5 N 1341 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7799 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1692 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2497 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "G" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 377 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2262 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'68H': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.96, per 1000 atoms: 0.64 Number of scatterers: 7799 At special positions: 0 Unit cell: (91.26, 95.316, 129.792, 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 48 16.00 O 1420 8.00 N 1341 7.00 C 4990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - 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: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 38.4% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.576A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.627A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.578A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.869A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.685A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.815A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.543A pdb=" N GLU A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.641A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.559A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 12 through 22 removed outlier: 3.989A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.759A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.633A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.899A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.178A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 40 removed outlier: 3.520A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 51 removed outlier: 3.923A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 59 removed outlier: 3.601A pdb=" N ILE R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 79 removed outlier: 3.960A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 77 " --> pdb=" O THR R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 86 removed outlier: 3.574A pdb=" N VAL R 86 " --> pdb=" O MET R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 105 through 137 removed outlier: 3.500A pdb=" N SER R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 141 removed outlier: 3.992A pdb=" N TYR R 141 " --> pdb=" O PRO R 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 138 through 141' Processing helix chain 'R' and resid 149 through 161 removed outlier: 3.974A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 208 through 220 removed outlier: 3.577A pdb=" N TYR R 219 " --> pdb=" O MET R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 237 removed outlier: 4.083A pdb=" N ARG R 228 " --> pdb=" O GLN R 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 274 removed outlier: 3.718A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 292 removed outlier: 3.751A pdb=" N MET R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR R 283 " --> pdb=" O MET R 279 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.013A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 314 Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.523A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix removed outlier: 3.536A pdb=" N TYR R 326 " --> pdb=" O ASN R 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 326' Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.650A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 245 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.650A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 245 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.672A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.673A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.848A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.677A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.872A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.766A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.888A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.569A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 5.662A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2504 1.34 - 1.46: 1921 1.46 - 1.58: 3468 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 7960 Sorted by residual: bond pdb=" CA THR A 263 " pdb=" CB THR A 263 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.68e+00 bond pdb=" C VAL R 87 " pdb=" N PRO R 88 " ideal model delta sigma weight residual 1.336 1.351 -0.016 1.23e-02 6.61e+03 1.64e+00 bond pdb=" N ARG R 239 " pdb=" CA ARG R 239 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.77e-02 3.19e+03 1.52e+00 bond pdb=" CB PRO R 211 " pdb=" CG PRO R 211 " ideal model delta sigma weight residual 1.492 1.431 0.061 5.00e-02 4.00e+02 1.48e+00 bond pdb=" N THR A 263 " pdb=" CA THR A 263 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.47e+00 ... (remaining 7955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 10442 1.75 - 3.51: 317 3.51 - 5.26: 45 5.26 - 7.01: 16 7.01 - 8.76: 6 Bond angle restraints: 10826 Sorted by residual: angle pdb=" N VAL R 31 " pdb=" CA VAL R 31 " pdb=" C VAL R 31 " ideal model delta sigma weight residual 113.53 109.05 4.48 9.80e-01 1.04e+00 2.09e+01 angle pdb=" C GLN A 262 " pdb=" N THR A 263 " pdb=" CA THR A 263 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" C ASP N 109 " pdb=" N VAL N 110 " pdb=" CA VAL N 110 " ideal model delta sigma weight residual 121.97 129.33 -7.36 1.80e+00 3.09e-01 1.67e+01 angle pdb=" C GLY R 238 " pdb=" N ARG R 239 " pdb=" CA ARG R 239 " ideal model delta sigma weight residual 125.66 133.15 -7.49 1.85e+00 2.92e-01 1.64e+01 angle pdb=" C HIS R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.70 128.26 -6.56 1.80e+00 3.09e-01 1.33e+01 ... (remaining 10821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4152 16.97 - 33.95: 421 33.95 - 50.92: 74 50.92 - 67.90: 13 67.90 - 84.87: 9 Dihedral angle restraints: 4669 sinusoidal: 1706 harmonic: 2963 Sorted by residual: dihedral pdb=" CA HIS R 178 " pdb=" C HIS R 178 " pdb=" N GLN R 179 " pdb=" CA GLN R 179 " ideal model delta harmonic sigma weight residual -180.00 -147.15 -32.85 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA GLY R 238 " pdb=" C GLY R 238 " pdb=" N ARG R 239 " pdb=" CA ARG R 239 " ideal model delta harmonic sigma weight residual -180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA THR R 177 " pdb=" C THR R 177 " pdb=" N HIS R 178 " pdb=" CA HIS R 178 " ideal model delta harmonic sigma weight residual 180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 4666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 878 0.049 - 0.097: 292 0.097 - 0.146: 76 0.146 - 0.195: 8 0.195 - 0.244: 1 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA THR A 263 " pdb=" N THR A 263 " pdb=" C THR A 263 " pdb=" CB THR A 263 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CB THR A 320 " pdb=" CA THR A 320 " pdb=" OG1 THR A 320 " pdb=" CG2 THR A 320 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 1252 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " -0.048 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO R 323 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO N 88 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " -0.040 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO R 211 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " -0.033 5.00e-02 4.00e+02 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2464 2.82 - 3.34: 6371 3.34 - 3.86: 12353 3.86 - 4.38: 14647 4.38 - 4.90: 25393 Nonbonded interactions: 61228 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.298 3.040 nonbonded pdb=" O ALA R 119 " pdb=" OG1 THR R 123 " model vdw 2.298 3.040 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.303 3.040 nonbonded pdb=" OG SER R 203 " pdb=" O2 68H R 401 " model vdw 2.306 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.308 3.040 ... (remaining 61223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.560 Find NCS groups from input model: 0.090 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 0.061 7960 Z= 0.254 Angle : 0.762 8.765 10826 Z= 0.424 Chirality : 0.051 0.244 1255 Planarity : 0.006 0.071 1367 Dihedral : 14.529 84.870 2743 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.13 % Allowed : 8.77 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.36 (0.19), residues: 999 helix: -4.75 (0.09), residues: 351 sheet: -2.28 (0.32), residues: 227 loop : -2.99 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.009 0.001 HIS A 357 PHE 0.017 0.002 PHE B 199 TYR 0.017 0.001 TYR B 59 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 0.922 Fit side-chains REVERT: A 16 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7775 (tt0) REVERT: A 236 GLN cc_start: 0.8367 (pt0) cc_final: 0.8074 (pt0) REVERT: A 336 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7849 (ttt180) REVERT: A 343 ASP cc_start: 0.7752 (m-30) cc_final: 0.7545 (m-30) REVERT: B 308 LEU cc_start: 0.8714 (pp) cc_final: 0.8496 (pt) REVERT: N 87 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8286 (mmtp) REVERT: N 118 ARG cc_start: 0.8493 (ttp-170) cc_final: 0.8272 (ttm170) REVERT: N 123 GLN cc_start: 0.8647 (tp40) cc_final: 0.8413 (tp40) REVERT: R 40 MET cc_start: 0.7860 (mtm) cc_final: 0.7501 (mtt) REVERT: R 224 GLN cc_start: 0.7392 (mt0) cc_final: 0.6990 (tm-30) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2405 time to fit residues: 61.7900 Evaluate side-chains 160 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 213 GLN A 218 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN B 156 GLN B 340 ASN N 3 GLN N 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7960 Z= 0.153 Angle : 0.534 5.599 10826 Z= 0.294 Chirality : 0.042 0.134 1255 Planarity : 0.004 0.046 1367 Dihedral : 6.443 83.261 1102 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.75 % Allowed : 14.54 % Favored : 83.71 % 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: -3.66 (0.23), residues: 999 helix: -2.48 (0.22), residues: 367 sheet: -1.72 (0.34), residues: 214 loop : -2.60 (0.26), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 109 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE R 289 TYR 0.009 0.001 TYR B 59 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 0.875 Fit side-chains REVERT: N 87 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8163 (mmtp) REVERT: N 118 ARG cc_start: 0.8461 (ttp-170) cc_final: 0.8253 (ttm170) REVERT: R 64 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8071 (pp) outliers start: 14 outliers final: 9 residues processed: 183 average time/residue: 0.2762 time to fit residues: 65.6868 Evaluate side-chains 160 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 340 ASN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7960 Z= 0.151 Angle : 0.498 5.465 10826 Z= 0.270 Chirality : 0.042 0.136 1255 Planarity : 0.003 0.044 1367 Dihedral : 6.094 79.662 1102 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.88 % Allowed : 17.42 % Favored : 79.70 % 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: -2.71 (0.24), residues: 999 helix: -1.10 (0.27), residues: 361 sheet: -1.58 (0.34), residues: 214 loop : -2.45 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE A 222 TYR 0.011 0.001 TYR B 85 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 0.793 Fit side-chains REVERT: A 343 ASP cc_start: 0.7964 (m-30) cc_final: 0.7689 (m-30) REVERT: N 87 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8149 (mmtp) REVERT: R 64 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8020 (pp) outliers start: 23 outliers final: 13 residues processed: 184 average time/residue: 0.2133 time to fit residues: 51.3839 Evaluate side-chains 164 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 142 HIS B 239 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 7960 Z= 0.447 Angle : 0.643 8.112 10826 Z= 0.345 Chirality : 0.047 0.149 1255 Planarity : 0.004 0.043 1367 Dihedral : 6.593 81.254 1102 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.88 % Allowed : 19.55 % Favored : 76.57 % 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: -2.47 (0.25), residues: 999 helix: -0.72 (0.28), residues: 354 sheet: -1.50 (0.34), residues: 215 loop : -2.44 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 47 HIS 0.009 0.002 HIS A 357 PHE 0.021 0.002 PHE A 222 TYR 0.024 0.002 TYR B 59 ARG 0.007 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 0.792 Fit side-chains REVERT: A 343 ASP cc_start: 0.8115 (m-30) cc_final: 0.7830 (m-30) REVERT: B 75 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8464 (tp40) REVERT: B 105 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8922 (t80) REVERT: B 234 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8166 (t80) REVERT: N 18 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7874 (tt) REVERT: N 87 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8176 (mmtp) REVERT: R 30 GLU cc_start: 0.6696 (tp30) cc_final: 0.6461 (tp30) REVERT: R 64 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8283 (pp) outliers start: 31 outliers final: 21 residues processed: 174 average time/residue: 0.2283 time to fit residues: 51.7474 Evaluate side-chains 173 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.0070 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7960 Z= 0.139 Angle : 0.511 9.084 10826 Z= 0.274 Chirality : 0.042 0.138 1255 Planarity : 0.003 0.042 1367 Dihedral : 5.943 75.992 1102 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.88 % Allowed : 20.80 % Favored : 75.31 % 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: -1.97 (0.26), residues: 999 helix: -0.23 (0.29), residues: 354 sheet: -1.33 (0.34), residues: 214 loop : -2.16 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 222 TYR 0.013 0.001 TYR B 85 ARG 0.010 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 0.812 Fit side-chains REVERT: A 24 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8393 (mmmt) REVERT: A 336 ARG cc_start: 0.7973 (ptm-80) cc_final: 0.7746 (ttt-90) REVERT: B 105 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8733 (t80) REVERT: B 234 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8136 (t80) REVERT: N 87 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8134 (mmtp) REVERT: R 64 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8170 (pp) outliers start: 31 outliers final: 21 residues processed: 175 average time/residue: 0.2167 time to fit residues: 50.3858 Evaluate side-chains 171 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 197 GLN Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7960 Z= 0.146 Angle : 0.496 5.942 10826 Z= 0.268 Chirality : 0.042 0.140 1255 Planarity : 0.003 0.044 1367 Dihedral : 5.439 62.133 1102 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.88 % Allowed : 20.80 % Favored : 75.31 % 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: -1.66 (0.26), residues: 999 helix: 0.14 (0.29), residues: 352 sheet: -1.19 (0.34), residues: 213 loop : -2.08 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE A 222 TYR 0.010 0.001 TYR B 59 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 0.943 Fit side-chains REVERT: A 336 ARG cc_start: 0.7994 (ptm-80) cc_final: 0.7726 (ttt180) REVERT: B 105 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8750 (t80) REVERT: B 118 ASP cc_start: 0.8190 (p0) cc_final: 0.7869 (p0) REVERT: B 234 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8045 (t80) REVERT: B 264 TYR cc_start: 0.9092 (m-80) cc_final: 0.8881 (m-80) REVERT: N 87 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8144 (mmtp) REVERT: R 64 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8089 (pp) outliers start: 31 outliers final: 21 residues processed: 175 average time/residue: 0.2115 time to fit residues: 49.3007 Evaluate side-chains 173 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 197 GLN Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.0970 chunk 81 optimal weight: 0.0870 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7960 Z= 0.188 Angle : 0.509 6.196 10826 Z= 0.276 Chirality : 0.043 0.142 1255 Planarity : 0.003 0.050 1367 Dihedral : 5.267 55.261 1102 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.88 % Allowed : 21.30 % Favored : 74.81 % 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: -1.52 (0.26), residues: 999 helix: 0.29 (0.29), residues: 352 sheet: -1.16 (0.34), residues: 214 loop : -2.00 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.001 PHE A 222 TYR 0.013 0.001 TYR B 59 ARG 0.017 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 336 ARG cc_start: 0.7950 (ptm-80) cc_final: 0.7688 (ttt180) REVERT: B 19 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.7174 (ttp-110) REVERT: B 105 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.8740 (t80) REVERT: B 118 ASP cc_start: 0.8245 (p0) cc_final: 0.7963 (p0) REVERT: B 234 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8090 (t80) REVERT: B 274 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8958 (p) REVERT: G 42 GLU cc_start: 0.8365 (tp30) cc_final: 0.8154 (tp30) REVERT: N 87 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8165 (mmtp) REVERT: R 40 MET cc_start: 0.7942 (mtm) cc_final: 0.7392 (mtt) REVERT: R 64 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8151 (pp) outliers start: 31 outliers final: 23 residues processed: 174 average time/residue: 0.2165 time to fit residues: 49.2732 Evaluate side-chains 176 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 197 GLN Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7960 Z= 0.152 Angle : 0.489 6.028 10826 Z= 0.264 Chirality : 0.042 0.140 1255 Planarity : 0.003 0.043 1367 Dihedral : 4.945 47.467 1102 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.63 % Allowed : 21.18 % Favored : 75.19 % 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: -1.31 (0.26), residues: 999 helix: 0.52 (0.30), residues: 352 sheet: -1.16 (0.34), residues: 218 loop : -1.85 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS A 357 PHE 0.024 0.001 PHE A 222 TYR 0.012 0.001 TYR N 60 ARG 0.013 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8582 (mm-30) REVERT: B 19 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.7297 (ttp-110) REVERT: B 105 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8731 (t80) REVERT: B 118 ASP cc_start: 0.8144 (p0) cc_final: 0.7839 (p0) REVERT: B 234 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8061 (t80) REVERT: B 274 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8961 (p) REVERT: N 87 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8126 (mmtp) REVERT: N 118 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8192 (ttm170) REVERT: R 40 MET cc_start: 0.7921 (mtm) cc_final: 0.7378 (mtt) REVERT: R 64 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8167 (pp) outliers start: 29 outliers final: 20 residues processed: 183 average time/residue: 0.2397 time to fit residues: 57.2476 Evaluate side-chains 181 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7960 Z= 0.152 Angle : 0.499 6.652 10826 Z= 0.270 Chirality : 0.042 0.148 1255 Planarity : 0.003 0.056 1367 Dihedral : 4.704 45.543 1102 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.63 % Allowed : 22.06 % Favored : 74.31 % 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: -1.17 (0.27), residues: 999 helix: 0.63 (0.30), residues: 352 sheet: -1.06 (0.34), residues: 218 loop : -1.80 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.010 0.001 PHE A 222 TYR 0.013 0.001 TYR B 59 ARG 0.020 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 HIS cc_start: 0.6977 (OUTLIER) cc_final: 0.6683 (t-170) REVERT: A 372 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.7990 (mp) REVERT: B 105 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.8718 (t80) REVERT: B 118 ASP cc_start: 0.8135 (p0) cc_final: 0.7859 (p0) REVERT: B 234 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8064 (t80) REVERT: B 274 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8909 (p) REVERT: N 39 GLN cc_start: 0.8360 (tt0) cc_final: 0.8152 (tt0) REVERT: N 60 TYR cc_start: 0.8852 (m-80) cc_final: 0.8527 (m-80) REVERT: N 87 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8152 (mmtp) REVERT: N 118 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8193 (ttm170) REVERT: R 40 MET cc_start: 0.7966 (mtm) cc_final: 0.7407 (mtt) REVERT: R 64 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8176 (pp) outliers start: 29 outliers final: 19 residues processed: 182 average time/residue: 0.2183 time to fit residues: 52.3212 Evaluate side-chains 180 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7960 Z= 0.151 Angle : 0.508 7.085 10826 Z= 0.272 Chirality : 0.042 0.140 1255 Planarity : 0.003 0.053 1367 Dihedral : 4.616 44.825 1102 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.01 % Allowed : 22.93 % Favored : 74.06 % 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: -1.10 (0.27), residues: 999 helix: 0.76 (0.30), residues: 352 sheet: -1.03 (0.35), residues: 212 loop : -1.81 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.012 0.001 TYR N 60 ARG 0.018 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8556 (mm-30) REVERT: A 372 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.7979 (mp) REVERT: B 19 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.7062 (ttp-110) REVERT: B 75 GLN cc_start: 0.8993 (tp40) cc_final: 0.8479 (tp40) REVERT: B 105 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8710 (t80) REVERT: B 118 ASP cc_start: 0.8155 (p0) cc_final: 0.7832 (p0) REVERT: B 234 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8060 (t80) REVERT: B 274 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8917 (p) REVERT: N 39 GLN cc_start: 0.8370 (tt0) cc_final: 0.8149 (tt0) REVERT: N 60 TYR cc_start: 0.8859 (m-80) cc_final: 0.8537 (m-80) REVERT: N 87 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8142 (mmtp) REVERT: N 118 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8168 (ttm170) REVERT: R 40 MET cc_start: 0.7954 (mtm) cc_final: 0.7399 (mtt) REVERT: R 64 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8171 (pp) outliers start: 24 outliers final: 17 residues processed: 173 average time/residue: 0.2121 time to fit residues: 48.1586 Evaluate side-chains 173 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 69 optimal weight: 0.0070 chunk 4 optimal weight: 0.0970 chunk 57 optimal weight: 6.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN N 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114595 restraints weight = 10490.775| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.19 r_work: 0.3151 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7960 Z= 0.118 Angle : 0.486 6.756 10826 Z= 0.261 Chirality : 0.042 0.139 1255 Planarity : 0.003 0.051 1367 Dihedral : 4.334 42.031 1102 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.01 % Allowed : 22.56 % 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: -0.93 (0.27), residues: 999 helix: 0.87 (0.30), residues: 356 sheet: -0.94 (0.35), residues: 212 loop : -1.71 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.000 HIS A 220 PHE 0.008 0.001 PHE R 208 TYR 0.011 0.001 TYR N 60 ARG 0.018 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.59 seconds wall clock time: 37 minutes 9.81 seconds (2229.81 seconds total)