Starting phenix.real_space_refine on Thu Nov 14 21:56:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/11_2024/8jlz_36409.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/11_2024/8jlz_36409.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/11_2024/8jlz_36409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/11_2024/8jlz_36409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/11_2024/8jlz_36409.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlz_36409/11_2024/8jlz_36409.cif" } 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. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7730 Number of models: 1 Model: "" Number of chains: 6 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: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1977 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 252} 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 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'UQL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.57, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 24 helices and 10 sheets defined 40.0% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.974A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.705A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.835A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 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 306 through 312 removed outlier: 3.795A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 312' Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.658A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 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) removed outlier: 3.582A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.629A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.594A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.949A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.585A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.795A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 54 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 59 through 61 No H-bonds generated for 'chain 'R' and resid 59 through 61' Processing helix chain 'R' and resid 62 through 77 removed outlier: 3.814A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.576A pdb=" N ALA R 83 " --> pdb=" O VAL R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 129 removed outlier: 4.489A pdb=" N LEU R 101 " --> pdb=" O GLY R 97 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU R 117 " --> pdb=" O SER R 113 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS R 118 " --> pdb=" O ILE R 114 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU R 119 " --> pdb=" O LEU R 115 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 126 " --> pdb=" O LEU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 165 Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 185 through 224 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 removed outlier: 3.501A pdb=" N SER R 224 " --> pdb=" O VAL R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 294 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 300 through 320 removed outlier: 3.707A pdb=" N VAL R 304 " --> pdb=" O GLY R 300 " (cutoff:3.500A) 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 Processing helix chain 'R' and resid 321 through 323 No H-bonds generated for 'chain 'R' and resid 321 through 323' Processing helix chain 'R' and resid 324 through 332 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 4.669A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 62 removed outlier: 4.016A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (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) Processing sheet with id=AA3, 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: 6.434A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.710A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA6, 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=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.685A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (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=AA8, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.850A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.369A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) 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) 368 hydrogen bonds defined for protein. 1065 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: 2.17 Time building geometry restraints manager: 2.12 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=" N1 UQL R 501 " ideal model delta sigma weight residual 1.384 1.258 0.126 2.00e-02 2.50e+03 3.98e+01 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=" C4 UQL R 501 " pdb=" C8 UQL R 501 " ideal model delta sigma weight residual 1.437 1.382 0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C3 UQL R 501 " pdb=" C4 UQL R 501 " ideal model delta sigma weight residual 1.421 1.462 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C7 UQL R 501 " pdb=" C9 UQL R 501 " ideal model delta sigma weight residual 1.488 1.524 -0.036 2.00e-02 2.50e+03 3.24e+00 ... (remaining 7879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 10602 2.57 - 5.13: 100 5.13 - 7.70: 8 7.70 - 10.26: 6 10.26 - 12.83: 1 Bond angle restraints: 10717 Sorted by residual: 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=" C4 UQL R 501 " pdb=" C8 UQL R 501 " pdb=" C7 UQL R 501 " ideal model delta sigma weight residual 106.60 119.43 -12.83 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N ASP A 284 " pdb=" CA ASP A 284 " pdb=" C ASP A 284 " ideal model delta sigma weight residual 114.56 110.35 4.21 1.27e+00 6.20e-01 1.10e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 108.86 113.29 -4.43 1.41e+00 5.03e-01 9.89e+00 angle pdb=" C5 UQL R 501 " pdb=" C4 UQL R 501 " pdb=" C8 UQL R 501 " ideal model delta sigma weight residual 133.36 142.64 -9.28 3.00e+00 1.11e-01 9.58e+00 ... (remaining 10712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4225 16.36 - 32.72: 345 32.72 - 49.08: 91 49.08 - 65.44: 12 65.44 - 81.80: 11 Dihedral angle restraints: 4684 sinusoidal: 1746 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 4681 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: 248 2.72 - 3.26: 7458 3.26 - 3.81: 11670 3.81 - 4.35: 13997 4.35 - 4.90: 24766 Nonbonded interactions: 58139 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.170 3.040 nonbonded pdb=" O PRO A 361 " pdb=" ND1 HIS A 362 " model vdw 2.201 3.120 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.283 3.120 nonbonded pdb=" O MET R 276 " pdb=" OG1 THR R 280 " model vdw 2.285 3.040 nonbonded pdb=" NH1 ARG N 67 " pdb=" O SER N 85 " model vdw 2.300 3.120 ... (remaining 58134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.070 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- 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 0.126 7884 Z= 0.313 Angle : 0.710 12.829 10717 Z= 0.391 Chirality : 0.044 0.209 1245 Planarity : 0.006 0.098 1363 Dihedral : 13.325 81.800 2768 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 to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 1.133 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: 0.2637 time to fit residues: 54.2649 Evaluate side-chains 152 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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: 0.9990 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7884 Z= 0.221 Angle : 0.556 5.704 10717 Z= 0.298 Chirality : 0.042 0.173 1245 Planarity : 0.005 0.069 1363 Dihedral : 4.562 17.182 1092 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.86 % Allowed : 9.14 % Favored : 90.00 % 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: -0.06 (0.27), residues: 997 helix: 1.31 (0.28), residues: 374 sheet: -0.15 (0.34), residues: 235 loop : -1.29 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.006 0.002 HIS A 220 PHE 0.016 0.002 PHE B 278 TYR 0.020 0.002 TYR R 320 ARG 0.003 0.000 ARG N 67 *********************** 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 167 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.838 Fit side-chains REVERT: A 392 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7077 (mm-30) REVERT: R 35 VAL cc_start: 0.8713 (p) cc_final: 0.8482 (m) REVERT: R 74 MET cc_start: 0.6354 (tmm) cc_final: 0.6029 (tmm) REVERT: R 276 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6296 (tpp) outliers start: 7 outliers final: 2 residues processed: 162 average time/residue: 0.2615 time to fit residues: 53.7571 Evaluate side-chains 159 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain R residue 276 MET 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: 4.9990 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.0070 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7884 Z= 0.155 Angle : 0.491 5.473 10717 Z= 0.260 Chirality : 0.040 0.152 1245 Planarity : 0.004 0.067 1363 Dihedral : 4.143 15.709 1092 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.73 % Allowed : 12.10 % Favored : 86.17 % 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: 0.29 (0.27), residues: 997 helix: 1.70 (0.28), residues: 376 sheet: 0.13 (0.35), residues: 233 loop : -1.29 (0.30), residues: 388 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 0.010 0.001 PHE B 278 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG B 251 *********************** 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 171 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.832 Fit side-chains REVERT: A 392 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 219 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7350 (mtt90) REVERT: B 291 ASP cc_start: 0.6999 (p0) cc_final: 0.6772 (p0) REVERT: B 331 SER cc_start: 0.8047 (t) cc_final: 0.7725 (p) REVERT: R 35 VAL cc_start: 0.8562 (p) cc_final: 0.8359 (m) REVERT: R 74 MET cc_start: 0.6250 (tmm) cc_final: 0.5865 (tmm) REVERT: R 210 ARG cc_start: 0.7100 (mmt90) cc_final: 0.6819 (mmt90) outliers start: 14 outliers final: 10 residues processed: 162 average time/residue: 0.2531 time to fit residues: 52.2767 Evaluate side-chains 161 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 246 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 156 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 0.0040 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1565 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= 0.152 Angle : 0.481 5.260 10717 Z= 0.254 Chirality : 0.040 0.145 1245 Planarity : 0.004 0.065 1363 Dihedral : 4.028 15.964 1092 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.35 % Allowed : 14.20 % Favored : 83.46 % 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: 0.54 (0.28), residues: 997 helix: 1.90 (0.28), residues: 377 sheet: 0.25 (0.35), residues: 233 loop : -1.14 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE A 376 TYR 0.012 0.001 TYR A 37 ARG 0.003 0.000 ARG B 251 *********************** 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 171 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.879 Fit side-chains REVERT: B 291 ASP cc_start: 0.6980 (p0) cc_final: 0.6754 (p0) REVERT: R 74 MET cc_start: 0.6206 (tmm) cc_final: 0.5893 (tmm) REVERT: R 210 ARG cc_start: 0.7110 (mmt90) cc_final: 0.6827 (mmt90) REVERT: R 276 MET cc_start: 0.6554 (tpp) cc_final: 0.6234 (tpp) outliers start: 19 outliers final: 12 residues processed: 163 average time/residue: 0.2570 time to fit residues: 53.5583 Evaluate side-chains 162 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 281 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.0370 chunk 39 optimal weight: 0.2980 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 0.0470 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7884 Z= 0.135 Angle : 0.462 5.136 10717 Z= 0.244 Chirality : 0.039 0.139 1245 Planarity : 0.004 0.064 1363 Dihedral : 3.918 18.198 1092 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.85 % Allowed : 15.56 % 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: 0.72 (0.28), residues: 997 helix: 2.08 (0.28), residues: 377 sheet: 0.24 (0.35), residues: 234 loop : -0.99 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.008 0.001 PHE B 241 TYR 0.011 0.001 TYR A 37 ARG 0.003 0.000 ARG A 38 *********************** 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 168 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.873 Fit side-chains REVERT: A 213 GLN cc_start: 0.7285 (pt0) cc_final: 0.7079 (pp30) REVERT: B 52 ARG cc_start: 0.7302 (mtt90) cc_final: 0.7057 (mtt90) REVERT: B 291 ASP cc_start: 0.6927 (p0) cc_final: 0.6677 (p0) REVERT: N 4 LEU cc_start: 0.7838 (mp) cc_final: 0.7525 (mt) REVERT: R 74 MET cc_start: 0.6141 (tmm) cc_final: 0.5654 (tmm) REVERT: R 108 MET cc_start: 0.6197 (ttp) cc_final: 0.5952 (ttt) REVERT: R 210 ARG cc_start: 0.7111 (mmt90) cc_final: 0.6802 (mmt90) REVERT: R 276 MET cc_start: 0.6436 (tpp) cc_final: 0.6175 (tpp) outliers start: 15 outliers final: 11 residues processed: 164 average time/residue: 0.2367 time to fit residues: 49.9250 Evaluate side-chains 161 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 133 ARG 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: 9.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 91 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7884 Z= 0.171 Angle : 0.496 6.567 10717 Z= 0.258 Chirality : 0.040 0.149 1245 Planarity : 0.004 0.062 1363 Dihedral : 3.981 17.815 1092 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.35 % Allowed : 15.80 % Favored : 81.85 % 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: 0.81 (0.28), residues: 997 helix: 2.15 (0.28), residues: 378 sheet: 0.34 (0.34), residues: 238 loop : -0.98 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE B 199 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG A 38 *********************** 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 169 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.864 Fit side-chains REVERT: B 152 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 291 ASP cc_start: 0.7002 (p0) cc_final: 0.6785 (p0) REVERT: N 71 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7868 (m) REVERT: R 74 MET cc_start: 0.6136 (tmm) cc_final: 0.5842 (tmm) REVERT: R 210 ARG cc_start: 0.7079 (mmt90) cc_final: 0.6770 (mmt90) outliers start: 19 outliers final: 15 residues processed: 162 average time/residue: 0.2576 time to fit residues: 52.7416 Evaluate side-chains 164 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER 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 281 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 77 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 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: 0.7980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7884 Z= 0.161 Angle : 0.487 6.381 10717 Z= 0.254 Chirality : 0.040 0.176 1245 Planarity : 0.004 0.062 1363 Dihedral : 3.938 17.151 1092 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.98 % Allowed : 16.79 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.28), residues: 997 helix: 2.19 (0.28), residues: 380 sheet: 0.29 (0.35), residues: 237 loop : -0.92 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE B 234 TYR 0.012 0.001 TYR A 37 ARG 0.004 0.000 ARG A 38 *********************** 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 168 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.848 Fit side-chains REVERT: A 284 ASP cc_start: 0.6535 (t0) cc_final: 0.6167 (t0) REVERT: B 152 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8033 (mp) REVERT: R 210 ARG cc_start: 0.7081 (mmt90) cc_final: 0.6779 (mmt90) outliers start: 16 outliers final: 15 residues processed: 162 average time/residue: 0.2608 time to fit residues: 53.8941 Evaluate side-chains 167 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER 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 281 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 77 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 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: 1.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7884 Z= 0.255 Angle : 0.557 7.729 10717 Z= 0.290 Chirality : 0.042 0.177 1245 Planarity : 0.004 0.060 1363 Dihedral : 4.248 17.350 1092 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.22 % Allowed : 17.65 % 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: 0.74 (0.28), residues: 997 helix: 2.05 (0.28), residues: 380 sheet: 0.30 (0.35), residues: 233 loop : -0.99 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 36 HIS 0.006 0.002 HIS A 220 PHE 0.017 0.002 PHE B 234 TYR 0.015 0.002 TYR A 37 ARG 0.004 0.000 ARG A 38 *********************** 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 169 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.884 Fit side-chains REVERT: A 284 ASP cc_start: 0.6629 (t0) cc_final: 0.6228 (t0) REVERT: B 152 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8125 (mp) REVERT: R 210 ARG cc_start: 0.7092 (mmt90) cc_final: 0.6792 (mmt90) outliers start: 18 outliers final: 14 residues processed: 161 average time/residue: 0.2597 time to fit residues: 53.6025 Evaluate side-chains 166 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 77 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 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: 1.9990 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7884 Z= 0.207 Angle : 0.539 8.419 10717 Z= 0.279 Chirality : 0.041 0.160 1245 Planarity : 0.004 0.060 1363 Dihedral : 4.178 16.596 1092 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.22 % Allowed : 17.78 % Favored : 80.00 % 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: 0.76 (0.28), residues: 997 helix: 2.20 (0.28), residues: 373 sheet: 0.30 (0.35), residues: 228 loop : -1.05 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.007 0.002 HIS A 220 PHE 0.014 0.001 PHE B 234 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG B 251 *********************** 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 172 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.895 Fit side-chains REVERT: A 284 ASP cc_start: 0.6610 (t0) cc_final: 0.6182 (t0) REVERT: B 220 GLN cc_start: 0.7774 (mt0) cc_final: 0.7570 (mt0) REVERT: R 210 ARG cc_start: 0.7084 (mmt90) cc_final: 0.6785 (mmt90) outliers start: 18 outliers final: 15 residues processed: 164 average time/residue: 0.2614 time to fit residues: 54.3757 Evaluate side-chains 170 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 133 ARG 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: 0.2980 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7884 Z= 0.171 Angle : 0.527 8.504 10717 Z= 0.271 Chirality : 0.040 0.187 1245 Planarity : 0.004 0.059 1363 Dihedral : 4.047 18.242 1092 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.73 % Allowed : 18.15 % 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: 0.81 (0.28), residues: 997 helix: 2.16 (0.28), residues: 380 sheet: 0.33 (0.34), residues: 235 loop : -1.00 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.007 0.001 HIS A 220 PHE 0.013 0.001 PHE A 222 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG B 251 ********************** 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 171 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.800 Fit side-chains REVERT: A 284 ASP cc_start: 0.6597 (t0) cc_final: 0.6164 (t0) REVERT: B 220 GLN cc_start: 0.7766 (mt0) cc_final: 0.7547 (mt0) REVERT: R 210 ARG cc_start: 0.7081 (mmt90) cc_final: 0.6786 (mmt90) outliers start: 14 outliers final: 13 residues processed: 166 average time/residue: 0.2622 time to fit residues: 55.3753 Evaluate side-chains 170 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 270 LEU 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 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 122 LEU 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: 2.9990 chunk 11 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117920 restraints weight = 11120.302| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.07 r_work: 0.3390 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7884 Z= 0.263 Angle : 0.582 9.532 10717 Z= 0.299 Chirality : 0.043 0.167 1245 Planarity : 0.004 0.058 1363 Dihedral : 4.315 16.415 1092 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.85 % Allowed : 18.27 % 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: 0.72 (0.28), residues: 997 helix: 2.12 (0.28), residues: 373 sheet: 0.26 (0.35), residues: 230 loop : -1.01 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.007 0.002 HIS A 220 PHE 0.018 0.002 PHE B 234 TYR 0.015 0.002 TYR A 37 ARG 0.004 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.93 seconds wall clock time: 39 minutes 24.51 seconds (2364.51 seconds total)