Starting phenix.real_space_refine on Mon Mar 11 14:45:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmh_24570/03_2024/7rmh_24570_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmh_24570/03_2024/7rmh_24570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmh_24570/03_2024/7rmh_24570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmh_24570/03_2024/7rmh_24570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmh_24570/03_2024/7rmh_24570_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmh_24570/03_2024/7rmh_24570_updated.pdb" } resolution = 3.1 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= -0.002 sd= 0.314 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1082 atoms to isotropic. 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 55 5.16 5 C 4811 2.51 5 N 1267 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7434 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1665 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain breaks: 4 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2319 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 245 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 851 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2269 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "S" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 85 Unusual residues: {'NH2': 1} Classifications: {'peptide': 11, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 8} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.42, per 1000 atoms: 0.59 Number of scatterers: 7434 At special positions: 0 Unit cell: (75.68, 98.9, 131.58, 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 55 16.00 O 1301 8.00 N 1267 7.00 C 4811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 11 sheets defined 36.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 3.511A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.508A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 60' Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 333 through 350 removed outlier: 4.214A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 4.073A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 29 through 59 removed outlier: 4.161A pdb=" N ILE R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 84 removed outlier: 3.640A pdb=" N TYR R 69 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE R 70 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER R 80 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE R 84 " --> pdb=" O MET R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 93 Processing helix chain 'R' and resid 102 through 134 Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 144 through 167 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 206 through 223 Processing helix chain 'R' and resid 240 through 272 Proline residue: R 263 - end of helix Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 275 through 278 removed outlier: 4.022A pdb=" N TYR R 278 " --> pdb=" O PRO R 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 275 through 278' Processing helix chain 'R' and resid 281 through 298 removed outlier: 4.397A pdb=" N SER R 297 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N THR R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 308 Processing helix chain 'R' and resid 310 through 319 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.366A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.123A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.063A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.890A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.951A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.773A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.560A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.799A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.188A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 169 through 174 347 hydrogen bonds defined for protein. 969 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: 2.20 Time building geometry restraints manager: 3.06 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: 2331 1.34 - 1.46: 1967 1.46 - 1.59: 3234 1.59 - 1.71: 0 1.71 - 1.83: 79 Bond restraints: 7611 Sorted by residual: bond pdb=" N GLN R 24 " pdb=" CA GLN R 24 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.33e-02 5.65e+03 8.92e+00 bond pdb=" C ARG S 1 " pdb=" N PRO S 2 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.41e+00 bond pdb=" CB PRO R 208 " pdb=" CG PRO R 208 " ideal model delta sigma weight residual 1.492 1.403 0.089 5.00e-02 4.00e+02 3.18e+00 bond pdb=" CA LEU R 262 " pdb=" C LEU R 262 " ideal model delta sigma weight residual 1.521 1.539 -0.017 1.08e-02 8.57e+03 2.62e+00 bond pdb=" C PHE R 163 " pdb=" N PRO R 164 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.25e-02 6.40e+03 2.24e+00 ... (remaining 7606 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.26: 166 106.26 - 113.23: 4087 113.23 - 120.19: 2739 120.19 - 127.15: 3296 127.15 - 134.11: 93 Bond angle restraints: 10381 Sorted by residual: angle pdb=" N PHE R 111 " pdb=" CA PHE R 111 " pdb=" C PHE R 111 " ideal model delta sigma weight residual 109.81 118.30 -8.49 2.21e+00 2.05e-01 1.47e+01 angle pdb=" N LEU R 270 " pdb=" CA LEU R 270 " pdb=" C LEU R 270 " ideal model delta sigma weight residual 112.75 116.95 -4.20 1.36e+00 5.41e-01 9.54e+00 angle pdb=" CA TRP B 169 " pdb=" CB TRP B 169 " pdb=" CG TRP B 169 " ideal model delta sigma weight residual 113.60 119.05 -5.45 1.90e+00 2.77e-01 8.23e+00 angle pdb=" N ASN R 301 " pdb=" CA ASN R 301 " pdb=" C ASN R 301 " ideal model delta sigma weight residual 109.81 115.85 -6.04 2.21e+00 2.05e-01 7.47e+00 angle pdb=" CA ARG R 141 " pdb=" CB ARG R 141 " pdb=" CG ARG R 141 " ideal model delta sigma weight residual 114.10 119.53 -5.43 2.00e+00 2.50e-01 7.38e+00 ... (remaining 10376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 3987 16.80 - 33.61: 340 33.61 - 50.41: 72 50.41 - 67.22: 8 67.22 - 84.02: 5 Dihedral angle restraints: 4412 sinusoidal: 1520 harmonic: 2892 Sorted by residual: dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -153.35 -26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+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 -157.70 -22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 4409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 806 0.043 - 0.086: 295 0.086 - 0.130: 86 0.130 - 0.173: 20 0.173 - 0.216: 3 Chirality restraints: 1210 Sorted by residual: chirality pdb=" CB VAL R 200 " pdb=" CA VAL R 200 " pdb=" CG1 VAL R 200 " pdb=" CG2 VAL R 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA PHE R 111 " pdb=" N PHE R 111 " pdb=" C PHE R 111 " pdb=" CB PHE R 111 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CG LEU B 284 " pdb=" CB LEU B 284 " pdb=" CD1 LEU B 284 " pdb=" CD2 LEU B 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 1207 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 174 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO R 175 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO N 88 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 224 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C VAL A 224 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 224 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 225 " -0.011 2.00e-02 2.50e+03 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2016 2.81 - 3.33: 5965 3.33 - 3.86: 11603 3.86 - 4.38: 12781 4.38 - 4.90: 23763 Nonbonded interactions: 56128 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.290 2.440 nonbonded pdb=" O ALA R 36 " pdb=" OG1 THR R 40 " model vdw 2.307 2.440 nonbonded pdb=" OE1 GLN N 39 " pdb=" OH TYR N 95 " model vdw 2.354 2.440 nonbonded pdb=" O LEU B 168 " pdb=" OG1 THR B 177 " model vdw 2.368 2.440 nonbonded pdb=" NH1 ARG N 67 " pdb=" O SER N 85 " model vdw 2.406 2.520 ... (remaining 56123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 7.310 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.280 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 0.089 7611 Z= 0.242 Angle : 0.747 8.487 10381 Z= 0.413 Chirality : 0.050 0.216 1210 Planarity : 0.005 0.051 1295 Dihedral : 13.417 84.023 2527 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.32 (0.25), residues: 958 helix: -0.93 (0.23), residues: 366 sheet: 0.50 (0.34), residues: 228 loop : -1.60 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.019 0.002 PHE R 264 TYR 0.012 0.001 TYR N 95 ARG 0.004 0.000 ARG R 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 247 ASP cc_start: 0.7784 (p0) cc_final: 0.7549 (p0) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1972 time to fit residues: 38.4281 Evaluate side-chains 95 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.0000 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 0.0470 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7611 Z= 0.168 Angle : 0.515 8.422 10381 Z= 0.274 Chirality : 0.041 0.140 1210 Planarity : 0.004 0.036 1295 Dihedral : 4.188 25.872 1059 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.24 % Allowed : 9.37 % Favored : 89.39 % 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: -0.39 (0.26), residues: 958 helix: 0.40 (0.27), residues: 365 sheet: 0.69 (0.34), residues: 221 loop : -1.49 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.003 0.001 HIS R 265 PHE 0.013 0.001 PHE R 264 TYR 0.011 0.001 TYR N 95 ARG 0.005 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 188 MET cc_start: 0.8109 (mmm) cc_final: 0.7764 (mmm) REVERT: N 68 PHE cc_start: 0.7434 (m-80) cc_final: 0.6800 (m-80) outliers start: 9 outliers final: 3 residues processed: 108 average time/residue: 0.1838 time to fit residues: 27.4238 Evaluate side-chains 96 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7611 Z= 0.268 Angle : 0.566 6.409 10381 Z= 0.305 Chirality : 0.043 0.187 1210 Planarity : 0.004 0.029 1295 Dihedral : 4.247 25.466 1059 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.24 % Allowed : 12.26 % Favored : 86.50 % 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: -0.18 (0.26), residues: 958 helix: 0.85 (0.28), residues: 358 sheet: 0.68 (0.33), residues: 221 loop : -1.58 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS R 95 PHE 0.019 0.002 PHE R 264 TYR 0.014 0.001 TYR N 95 ARG 0.006 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.862 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 108 average time/residue: 0.1783 time to fit residues: 26.8378 Evaluate side-chains 94 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7611 Z= 0.213 Angle : 0.526 6.286 10381 Z= 0.284 Chirality : 0.042 0.162 1210 Planarity : 0.004 0.040 1295 Dihedral : 4.162 28.186 1059 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.79 % Allowed : 14.33 % Favored : 83.88 % 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: 0.02 (0.27), residues: 958 helix: 1.17 (0.28), residues: 359 sheet: 0.65 (0.33), residues: 221 loop : -1.54 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 PHE 0.020 0.001 PHE N 68 TYR 0.012 0.001 TYR N 95 ARG 0.009 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.952 Fit side-chains REVERT: B 273 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7962 (mp) outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 0.1928 time to fit residues: 28.1519 Evaluate side-chains 100 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7611 Z= 0.171 Angle : 0.509 6.256 10381 Z= 0.272 Chirality : 0.042 0.153 1210 Planarity : 0.003 0.038 1295 Dihedral : 4.047 29.875 1059 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.07 % Allowed : 14.19 % Favored : 83.75 % 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: 0.21 (0.27), residues: 958 helix: 1.45 (0.28), residues: 356 sheet: 0.67 (0.33), residues: 221 loop : -1.49 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.000 HIS A 220 PHE 0.013 0.001 PHE R 264 TYR 0.010 0.001 TYR N 95 ARG 0.007 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7867 (mp) outliers start: 15 outliers final: 8 residues processed: 106 average time/residue: 0.1859 time to fit residues: 27.1664 Evaluate side-chains 101 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.0570 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7611 Z= 0.152 Angle : 0.497 6.425 10381 Z= 0.265 Chirality : 0.041 0.147 1210 Planarity : 0.003 0.036 1295 Dihedral : 4.048 30.531 1059 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.65 % Allowed : 16.80 % Favored : 81.54 % 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: 0.39 (0.27), residues: 958 helix: 1.65 (0.28), residues: 356 sheet: 0.65 (0.33), residues: 226 loop : -1.39 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.000 HIS A 220 PHE 0.012 0.001 PHE R 264 TYR 0.009 0.001 TYR N 60 ARG 0.008 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7864 (mp) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.1781 time to fit residues: 26.5274 Evaluate side-chains 103 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 0.0370 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7611 Z= 0.157 Angle : 0.497 6.704 10381 Z= 0.265 Chirality : 0.041 0.147 1210 Planarity : 0.003 0.035 1295 Dihedral : 3.948 30.611 1059 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.07 % Allowed : 17.08 % Favored : 80.85 % 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: 0.47 (0.27), residues: 958 helix: 1.74 (0.29), residues: 356 sheet: 0.65 (0.33), residues: 226 loop : -1.34 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.000 HIS A 220 PHE 0.013 0.001 PHE R 264 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7736 (tt) outliers start: 15 outliers final: 11 residues processed: 107 average time/residue: 0.1916 time to fit residues: 28.7702 Evaluate side-chains 105 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7611 Z= 0.179 Angle : 0.509 7.285 10381 Z= 0.272 Chirality : 0.042 0.150 1210 Planarity : 0.003 0.040 1295 Dihedral : 3.968 31.003 1059 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 1.79 % Allowed : 17.08 % Favored : 81.13 % 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: 0.47 (0.27), residues: 958 helix: 1.74 (0.28), residues: 358 sheet: 0.64 (0.33), residues: 226 loop : -1.35 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 PHE 0.019 0.001 PHE N 68 TYR 0.010 0.001 TYR N 95 ARG 0.009 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 273 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7848 (mp) outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 0.1762 time to fit residues: 25.9824 Evaluate side-chains 103 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7611 Z= 0.164 Angle : 0.509 7.104 10381 Z= 0.270 Chirality : 0.042 0.170 1210 Planarity : 0.003 0.037 1295 Dihedral : 3.956 32.248 1059 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 1.65 % Allowed : 17.08 % Favored : 81.27 % 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: 0.51 (0.27), residues: 958 helix: 1.73 (0.28), residues: 364 sheet: 0.69 (0.33), residues: 226 loop : -1.34 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 PHE 0.020 0.001 PHE A 222 TYR 0.010 0.001 TYR N 95 ARG 0.009 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 273 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7934 (mp) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 0.1904 time to fit residues: 27.1070 Evaluate side-chains 102 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7611 Z= 0.176 Angle : 0.516 7.764 10381 Z= 0.274 Chirality : 0.042 0.161 1210 Planarity : 0.003 0.042 1295 Dihedral : 3.956 32.564 1059 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 1.38 % Allowed : 17.77 % Favored : 80.85 % 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: 0.51 (0.27), residues: 958 helix: 1.76 (0.28), residues: 363 sheet: 0.71 (0.33), residues: 226 loop : -1.40 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 PHE 0.017 0.001 PHE A 222 TYR 0.010 0.001 TYR N 95 ARG 0.009 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7935 (mp) REVERT: G 21 MET cc_start: 0.6070 (tmm) cc_final: 0.5710 (tmm) outliers start: 10 outliers final: 9 residues processed: 100 average time/residue: 0.1887 time to fit residues: 26.1212 Evaluate side-chains 103 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 0.0570 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.121793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101324 restraints weight = 13726.783| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.64 r_work: 0.3292 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7611 Z= 0.135 Angle : 0.492 7.930 10381 Z= 0.259 Chirality : 0.041 0.156 1210 Planarity : 0.003 0.038 1295 Dihedral : 3.845 34.225 1059 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 1.10 % Allowed : 18.04 % Favored : 80.85 % 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: 0.68 (0.28), residues: 958 helix: 1.90 (0.28), residues: 363 sheet: 0.81 (0.34), residues: 224 loop : -1.30 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 PHE 0.013 0.001 PHE A 222 TYR 0.009 0.001 TYR N 60 ARG 0.009 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.31 seconds wall clock time: 32 minutes 31.01 seconds (1951.01 seconds total)