Starting phenix.real_space_refine on Sat Apr 6 08:30:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/04_2024/8jlz_36409_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/04_2024/8jlz_36409.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/04_2024/8jlz_36409_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/04_2024/8jlz_36409_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/04_2024/8jlz_36409_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/04_2024/8jlz_36409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/04_2024/8jlz_36409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/04_2024/8jlz_36409_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/04_2024/8jlz_36409_updated.pdb" } resolution = 3.09 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= 0.004 sd= 0.050 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 1 4.86 5 C 4917 2.51 5 N 1336 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "R PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7730 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1831 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2533 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 953 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 1993 Unusual residues: {'UQL': 1} Classifications: {'peptide': 268, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 252, None: 1} Not linked: pdbres="GLY R 332 " pdbres="UQL R 501 " Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 4.46, per 1000 atoms: 0.58 Number of scatterers: 7730 At special positions: 0 Unit cell: (96.05, 107.1, 116.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 56 16.00 O 1420 8.00 N 1336 7.00 C 4917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 99 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS R 294 " - pdb=" SG CYS R 296 " distance=2.03 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 10 sheets defined 36.7% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 removed outlier: 3.974A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.322A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 4.105A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.495A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'R' and resid 28 through 53 removed outlier: 3.848A pdb=" N VAL R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU R 39 " --> pdb=" O VAL R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 88 removed outlier: 4.640A pdb=" N PHE R 64 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU R 65 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL R 66 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU R 77 " --> pdb=" O MET R 74 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL R 78 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL R 79 " --> pdb=" O GLY R 76 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET R 80 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 96 through 128 removed outlier: 4.002A pdb=" N LEU R 100 " --> pdb=" O GLY R 97 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS R 110 " --> pdb=" O VAL R 107 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE R 114 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN R 116 " --> pdb=" O SER R 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS R 118 " --> pdb=" O LEU R 115 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE R 120 " --> pdb=" O LEU R 117 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG R 124 " --> pdb=" O SER R 121 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR R 125 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU R 126 " --> pdb=" O ASP R 123 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU R 127 " --> pdb=" O ARG R 124 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE R 128 " --> pdb=" O TYR R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 164 Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 186 through 223 removed outlier: 4.133A pdb=" N SER R 193 " --> pdb=" O VAL R 189 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 265 through 293 removed outlier: 3.788A pdb=" N PHE R 277 " --> pdb=" O LEU R 273 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 4.233A pdb=" N ILE R 289 " --> pdb=" O PHE R 285 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL R 290 " --> pdb=" O VAL R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 323 removed outlier: 3.807A pdb=" N LEU R 308 " --> pdb=" O VAL R 304 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER R 313 " --> pdb=" O GLY R 309 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR R 314 " --> pdb=" O TYR R 310 " (cutoff:3.500A) Proline residue: R 317 - end of helix Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 325 through 331 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.010A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.423A 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 62 removed outlier: 3.604A pdb=" N TYR B 59 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.397A 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: 7.236A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.632A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.104A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.422A 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: 7.076A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.145A 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: 6.536A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 336 through 339 removed outlier: 3.595A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (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 10 through 12 removed outlier: 3.522A pdb=" N VAL N 124 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA N 92 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 870 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: 2.08 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: 2524 1.34 - 1.46: 1884 1.46 - 1.59: 3398 1.59 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 7884 Sorted by residual: bond pdb=" C7 UQL R 501 " pdb=" C8 UQL R 501 " ideal model delta sigma weight residual 1.377 1.272 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C7 UQL R 501 " pdb=" N1 UQL R 501 " ideal model delta sigma weight residual 1.357 1.258 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C3 UQL R 501 " pdb=" C4 UQL R 501 " ideal model delta sigma weight residual 1.368 1.462 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C2 UQL R 501 " pdb=" C3 UQL R 501 " ideal model delta sigma weight residual 1.406 1.360 0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" C4 UQL R 501 " pdb=" C5 UQL R 501 " ideal model delta sigma weight residual 1.406 1.373 0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 7879 not shown) Histogram of bond angle deviations from ideal: 99.02 - 107.74: 266 107.74 - 116.47: 5084 116.47 - 125.19: 5240 125.19 - 133.92: 116 133.92 - 142.64: 11 Bond angle restraints: 10717 Sorted by residual: angle pdb=" C9 UQL R 501 " pdb=" C7 UQL R 501 " pdb=" N1 UQL R 501 " ideal model delta sigma weight residual 100.49 128.88 -28.39 3.00e+00 1.11e-01 8.96e+01 angle pdb=" C8 UQL R 501 " pdb=" C7 UQL R 501 " pdb=" C9 UQL R 501 " ideal model delta sigma weight residual 151.42 129.77 21.65 3.00e+00 1.11e-01 5.21e+01 angle pdb=" C ILE R 319 " pdb=" N TYR R 320 " pdb=" CA TYR R 320 " ideal model delta sigma weight residual 120.09 114.63 5.46 1.25e+00 6.40e-01 1.91e+01 angle pdb=" C10 UQL R 501 " pdb=" C8 UQL R 501 " pdb=" C4 UQL R 501 " ideal model delta sigma weight residual 132.69 120.69 12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C4 UQL R 501 " pdb=" C8 UQL R 501 " pdb=" C7 UQL R 501 " ideal model delta sigma weight residual 107.95 119.43 -11.48 3.00e+00 1.11e-01 1.46e+01 ... (remaining 10712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4221 16.36 - 32.72: 345 32.72 - 49.08: 93 49.08 - 65.44: 12 65.44 - 81.80: 11 Dihedral angle restraints: 4682 sinusoidal: 1744 harmonic: 2938 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -19.05 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS R 294 " pdb=" SG CYS R 294 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -140.57 54.57 1 1.00e+01 1.00e-02 4.04e+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 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 868 0.042 - 0.084: 292 0.084 - 0.126: 76 0.126 - 0.167: 8 0.167 - 0.209: 1 Chirality restraints: 1245 Sorted by residual: chirality pdb=" CA TYR R 320 " pdb=" N TYR R 320 " pdb=" C TYR R 320 " pdb=" CB TYR R 320 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ARG A 317 " pdb=" N ARG A 317 " pdb=" C ARG A 317 " pdb=" CB ARG A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1242 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 316 " 0.065 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO R 317 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO R 317 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO R 317 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 81 " -0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO R 82 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO R 82 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 82 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO G 49 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.034 5.00e-02 4.00e+02 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 252 2.72 - 3.26: 7489 3.26 - 3.81: 11654 3.81 - 4.35: 14086 4.35 - 4.90: 24786 Nonbonded interactions: 58267 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.170 2.440 nonbonded pdb=" O PRO A 361 " pdb=" ND1 HIS A 362 " model vdw 2.201 2.520 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.283 2.520 nonbonded pdb=" O MET R 276 " pdb=" OG1 THR R 280 " model vdw 2.285 2.440 nonbonded pdb=" NH1 ARG N 67 " pdb=" O SER N 85 " model vdw 2.300 2.520 ... (remaining 58262 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.060 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.500 Find NCS groups from input model: 0.200 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.005 0.105 7884 Z= 0.304 Angle : 0.786 28.393 10717 Z= 0.407 Chirality : 0.044 0.209 1245 Planarity : 0.006 0.098 1363 Dihedral : 13.378 81.800 2766 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.12 % Allowed : 0.25 % Favored : 99.63 % 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: -0.56 (0.27), residues: 997 helix: 0.64 (0.28), residues: 370 sheet: -0.20 (0.35), residues: 219 loop : -1.36 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.004 0.002 HIS A 41 PHE 0.019 0.002 PHE B 278 TYR 0.021 0.002 TYR R 320 ARG 0.007 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.740 Fit side-chains REVERT: A 392 GLU cc_start: 0.7239 (mm-30) cc_final: 0.7023 (mm-30) REVERT: R 35 VAL cc_start: 0.8814 (p) cc_final: 0.8591 (m) REVERT: R 74 MET cc_start: 0.6426 (tmm) cc_final: 0.6130 (tmm) REVERT: R 127 LEU cc_start: 0.8572 (tp) cc_final: 0.8273 (tp) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2575 time to fit residues: 52.7854 Evaluate side-chains 152 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.0060 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 29 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 218 ASN N 31 ASN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7884 Z= 0.144 Angle : 0.496 5.546 10717 Z= 0.261 Chirality : 0.040 0.173 1245 Planarity : 0.005 0.064 1363 Dihedral : 4.473 35.456 1090 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.74 % Allowed : 9.01 % Favored : 90.25 % 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: -0.25 (0.27), residues: 997 helix: 0.99 (0.28), residues: 367 sheet: -0.15 (0.34), residues: 238 loop : -1.23 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE B 278 TYR 0.021 0.001 TYR R 320 ARG 0.002 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 154 time to evaluate : 0.849 Fit side-chains REVERT: R 35 VAL cc_start: 0.8672 (p) cc_final: 0.8457 (m) REVERT: R 74 MET cc_start: 0.6320 (tmm) cc_final: 0.6081 (tmm) REVERT: R 127 LEU cc_start: 0.8547 (tp) cc_final: 0.8252 (tp) REVERT: R 210 ARG cc_start: 0.7053 (mmt90) cc_final: 0.6771 (mmt90) outliers start: 6 outliers final: 5 residues processed: 155 average time/residue: 0.2730 time to fit residues: 54.0650 Evaluate side-chains 156 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 133 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 279 ASN N 31 ASN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7884 Z= 0.159 Angle : 0.480 5.566 10717 Z= 0.253 Chirality : 0.040 0.152 1245 Planarity : 0.004 0.055 1363 Dihedral : 4.287 35.253 1090 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.73 % Allowed : 11.48 % Favored : 86.79 % 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: -0.10 (0.27), residues: 997 helix: 1.12 (0.28), residues: 367 sheet: -0.08 (0.34), residues: 233 loop : -1.14 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR A 37 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.884 Fit side-chains REVERT: B 61 MET cc_start: 0.7649 (ppp) cc_final: 0.6418 (ppp) REVERT: R 35 VAL cc_start: 0.8614 (p) cc_final: 0.8408 (m) REVERT: R 74 MET cc_start: 0.6184 (tmm) cc_final: 0.5945 (tmm) REVERT: R 127 LEU cc_start: 0.8525 (tp) cc_final: 0.8240 (tp) REVERT: R 210 ARG cc_start: 0.7058 (mmt90) cc_final: 0.6765 (mmt90) outliers start: 14 outliers final: 12 residues processed: 152 average time/residue: 0.2536 time to fit residues: 49.4214 Evaluate side-chains 155 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 133 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 0.0270 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 31 ASN N 74 ASN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7884 Z= 0.341 Angle : 0.571 5.672 10717 Z= 0.303 Chirality : 0.044 0.160 1245 Planarity : 0.005 0.052 1363 Dihedral : 4.772 39.269 1090 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.84 % Allowed : 13.33 % Favored : 83.83 % 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: -0.23 (0.27), residues: 997 helix: 1.02 (0.28), residues: 366 sheet: -0.18 (0.35), residues: 226 loop : -1.17 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.006 0.002 HIS A 220 PHE 0.021 0.002 PHE B 234 TYR 0.017 0.002 TYR A 37 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.085 Fit side-chains REVERT: A 284 ASP cc_start: 0.6636 (t0) cc_final: 0.6285 (t0) REVERT: A 392 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6999 (mm-30) REVERT: N 51 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7525 (tt) REVERT: R 74 MET cc_start: 0.6131 (tmm) cc_final: 0.5768 (tmm) REVERT: R 127 LEU cc_start: 0.8538 (tp) cc_final: 0.8254 (tp) REVERT: R 210 ARG cc_start: 0.7107 (mmt90) cc_final: 0.6862 (mmt90) outliers start: 23 outliers final: 18 residues processed: 163 average time/residue: 0.2704 time to fit residues: 55.9402 Evaluate side-chains 170 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 31 ASN N 74 ASN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7884 Z= 0.171 Angle : 0.481 5.471 10717 Z= 0.254 Chirality : 0.040 0.148 1245 Planarity : 0.004 0.054 1363 Dihedral : 4.386 35.530 1090 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.96 % Allowed : 14.44 % Favored : 82.59 % 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: 0.01 (0.27), residues: 997 helix: 1.22 (0.29), residues: 366 sheet: 0.00 (0.34), residues: 233 loop : -1.10 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 0.773 Fit side-chains REVERT: A 284 ASP cc_start: 0.6577 (t0) cc_final: 0.6230 (t0) REVERT: R 74 MET cc_start: 0.5997 (tmm) cc_final: 0.5658 (tmm) REVERT: R 210 ARG cc_start: 0.7102 (mmt90) cc_final: 0.6820 (mmt90) outliers start: 24 outliers final: 19 residues processed: 159 average time/residue: 0.2588 time to fit residues: 52.2791 Evaluate side-chains 162 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.0020 chunk 91 optimal weight: 4.9990 overall best weight: 1.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 31 ASN N 74 ASN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7884 Z= 0.257 Angle : 0.529 6.212 10717 Z= 0.278 Chirality : 0.042 0.154 1245 Planarity : 0.004 0.054 1363 Dihedral : 4.550 38.018 1090 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.47 % Allowed : 15.93 % Favored : 81.60 % 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: -0.03 (0.27), residues: 997 helix: 1.18 (0.29), residues: 366 sheet: -0.13 (0.34), residues: 236 loop : -1.03 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.006 0.002 HIS A 220 PHE 0.017 0.002 PHE B 234 TYR 0.017 0.002 TYR A 37 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.931 Fit side-chains REVERT: A 284 ASP cc_start: 0.6629 (t0) cc_final: 0.6238 (t0) REVERT: R 74 MET cc_start: 0.5948 (tmm) cc_final: 0.5566 (tmm) REVERT: R 210 ARG cc_start: 0.7107 (mmt90) cc_final: 0.6829 (mmt90) outliers start: 20 outliers final: 16 residues processed: 158 average time/residue: 0.2586 time to fit residues: 52.4977 Evaluate side-chains 164 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 59 optimal weight: 0.0470 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 0.0670 chunk 58 optimal weight: 0.0870 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 31 ASN N 74 ASN R 44 ASN R 291 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7884 Z= 0.123 Angle : 0.457 6.176 10717 Z= 0.237 Chirality : 0.039 0.135 1245 Planarity : 0.004 0.057 1363 Dihedral : 4.032 32.424 1090 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.59 % Allowed : 16.91 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 997 helix: 1.39 (0.29), residues: 366 sheet: 0.01 (0.34), residues: 228 loop : -1.03 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.009 0.001 PHE B 234 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.806 Fit side-chains REVERT: A 215 ASP cc_start: 0.6978 (t0) cc_final: 0.6701 (t0) REVERT: A 284 ASP cc_start: 0.6528 (t0) cc_final: 0.6157 (t0) REVERT: R 74 MET cc_start: 0.5912 (tmm) cc_final: 0.5654 (tmm) REVERT: R 210 ARG cc_start: 0.7055 (mmt90) cc_final: 0.6769 (mmt90) outliers start: 21 outliers final: 18 residues processed: 164 average time/residue: 0.2494 time to fit residues: 52.1149 Evaluate side-chains 164 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7884 Z= 0.167 Angle : 0.487 6.035 10717 Z= 0.252 Chirality : 0.040 0.150 1245 Planarity : 0.004 0.056 1363 Dihedral : 4.149 35.789 1090 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.47 % Allowed : 17.90 % Favored : 79.63 % 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: 0.22 (0.27), residues: 997 helix: 1.45 (0.29), residues: 366 sheet: 0.06 (0.34), residues: 229 loop : -0.99 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE B 234 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.890 Fit side-chains REVERT: A 215 ASP cc_start: 0.7015 (t0) cc_final: 0.6642 (t0) REVERT: A 284 ASP cc_start: 0.6584 (t0) cc_final: 0.6186 (t0) REVERT: R 74 MET cc_start: 0.5858 (tmm) cc_final: 0.5597 (tmm) REVERT: R 210 ARG cc_start: 0.7059 (mmt90) cc_final: 0.6783 (mmt90) outliers start: 20 outliers final: 19 residues processed: 156 average time/residue: 0.2593 time to fit residues: 51.3984 Evaluate side-chains 163 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 31 ASN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7884 Z= 0.295 Angle : 0.561 6.230 10717 Z= 0.294 Chirality : 0.043 0.192 1245 Planarity : 0.004 0.054 1363 Dihedral : 4.593 39.062 1090 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.96 % Allowed : 17.16 % Favored : 79.88 % 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: 0.10 (0.27), residues: 997 helix: 1.32 (0.29), residues: 363 sheet: -0.02 (0.34), residues: 236 loop : -1.00 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.002 HIS A 220 PHE 0.020 0.002 PHE B 234 TYR 0.016 0.002 TYR A 37 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 0.824 Fit side-chains REVERT: A 215 ASP cc_start: 0.7039 (t0) cc_final: 0.6662 (t0) REVERT: A 284 ASP cc_start: 0.6671 (t0) cc_final: 0.6217 (t0) REVERT: B 52 ARG cc_start: 0.7359 (mtt90) cc_final: 0.7138 (mtt90) REVERT: R 74 MET cc_start: 0.5849 (tmm) cc_final: 0.5541 (tmm) REVERT: R 210 ARG cc_start: 0.7080 (mmt90) cc_final: 0.6793 (mmt90) REVERT: R 276 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6210 (tpp) outliers start: 24 outliers final: 18 residues processed: 160 average time/residue: 0.2426 time to fit residues: 49.6774 Evaluate side-chains 168 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 31 ASN R 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7884 Z= 0.191 Angle : 0.511 5.883 10717 Z= 0.266 Chirality : 0.041 0.168 1245 Planarity : 0.004 0.057 1363 Dihedral : 4.357 36.535 1090 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.22 % Allowed : 17.53 % Favored : 80.25 % 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: 0.17 (0.27), residues: 997 helix: 1.38 (0.29), residues: 364 sheet: 0.08 (0.34), residues: 229 loop : -1.02 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE B 199 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG B 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 0.781 Fit side-chains REVERT: A 215 ASP cc_start: 0.7008 (t0) cc_final: 0.6628 (t0) REVERT: A 284 ASP cc_start: 0.6626 (t0) cc_final: 0.6177 (t0) REVERT: R 74 MET cc_start: 0.5900 (tmm) cc_final: 0.5598 (tmm) REVERT: R 210 ARG cc_start: 0.7059 (mmt90) cc_final: 0.6783 (mmt90) outliers start: 18 outliers final: 17 residues processed: 160 average time/residue: 0.2583 time to fit residues: 52.5937 Evaluate side-chains 166 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.0030 chunk 68 optimal weight: 0.8980 overall best weight: 0.6910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.141018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120367 restraints weight = 11151.452| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.11 r_work: 0.3435 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7884 Z= 0.158 Angle : 0.489 5.786 10717 Z= 0.253 Chirality : 0.040 0.169 1245 Planarity : 0.004 0.057 1363 Dihedral : 4.144 35.298 1090 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.10 % Allowed : 17.78 % Favored : 80.12 % 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: 0.30 (0.27), residues: 997 helix: 1.52 (0.29), residues: 364 sheet: 0.15 (0.34), residues: 224 loop : -0.96 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE B 234 TYR 0.014 0.001 TYR A 37 ARG 0.001 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.70 seconds wall clock time: 41 minutes 2.52 seconds (2462.52 seconds total)