Starting phenix.real_space_refine on Fri Nov 15 13:25:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpt_60354/11_2024/8zpt_60354.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpt_60354/11_2024/8zpt_60354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpt_60354/11_2024/8zpt_60354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpt_60354/11_2024/8zpt_60354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpt_60354/11_2024/8zpt_60354.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpt_60354/11_2024/8zpt_60354.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5827 2.51 5 N 1601 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 9151 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1875 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2577 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 403 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 161 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 3, 'TRANS': 16} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2352 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 5.41, per 1000 atoms: 0.59 Number of scatterers: 9151 At special positions: 0 Unit cell: (82.62, 123.12, 133.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1670 8.00 N 1601 7.00 C 5827 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.450A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.531A pdb=" N ARG A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.856A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 11 through 30 removed outlier: 3.583A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 removed outlier: 3.575A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.857A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.544A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'L' and resid 4 through 11 removed outlier: 4.148A pdb=" N SER L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.597A pdb=" N TYR R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA R 86 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 92 Processing helix chain 'R' and resid 93 through 123 Proline residue: R 115 - end of helix Processing helix chain 'R' and resid 132 through 164 removed outlier: 4.016A pdb=" N LEU R 136 " --> pdb=" O GLY R 132 " (cutoff:3.500A) Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 172 through 198 removed outlier: 3.612A pdb=" N SER R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 220 through 255 removed outlier: 3.640A pdb=" N LEU R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA R 226 " --> pdb=" O ARG R 222 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU R 229 " --> pdb=" O TYR R 225 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU R 236 " --> pdb=" O VAL R 232 " (cutoff:3.500A) Proline residue: R 237 - end of helix Processing helix chain 'R' and resid 267 through 304 removed outlier: 3.613A pdb=" N TRP R 291 " --> pdb=" O PHE R 287 " (cutoff:3.500A) Proline residue: R 293 - end of helix Processing helix chain 'R' and resid 309 through 336 removed outlier: 4.733A pdb=" N GLY R 314 " --> pdb=" O PRO R 310 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU R 315 " --> pdb=" O TYR R 311 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER R 327 " --> pdb=" O LEU R 323 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA R 328 " --> pdb=" O ALA R 324 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.503A pdb=" N ALA R 336 " --> pdb=" O PRO R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.805A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.709A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 341 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 7.028A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.904A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.533A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.843A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.585A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.809A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.154A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.154A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 97 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.606A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.539A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 199 through 201 450 hydrogen bonds defined for protein. 1257 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: 2.71 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2993 1.34 - 1.46: 2178 1.46 - 1.58: 4104 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9349 Sorted by residual: bond pdb=" N ALA A 7 " pdb=" CA ALA A 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N ASP B 10 " pdb=" CA ASP B 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ALA G 9 " pdb=" CA ALA G 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N VAL E 1 " pdb=" CA VAL E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N THR L 1 " pdb=" CA THR L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 9344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 12231 0.99 - 1.97: 366 1.97 - 2.96: 51 2.96 - 3.95: 36 3.95 - 4.93: 6 Bond angle restraints: 12690 Sorted by residual: angle pdb=" N ARG B 73 " pdb=" CA ARG B 73 " pdb=" C ARG B 73 " ideal model delta sigma weight residual 113.43 110.06 3.37 1.26e+00 6.30e-01 7.15e+00 angle pdb=" N THR B 92 " pdb=" CA THR B 92 " pdb=" CB THR B 92 " ideal model delta sigma weight residual 113.65 109.90 3.75 1.47e+00 4.63e-01 6.52e+00 angle pdb=" N THR B 201 " pdb=" CA THR B 201 " pdb=" CB THR B 201 " ideal model delta sigma weight residual 113.65 110.30 3.35 1.47e+00 4.63e-01 5.20e+00 angle pdb=" N GLN R 58 " pdb=" CA GLN R 58 " pdb=" CB GLN R 58 " ideal model delta sigma weight residual 113.65 110.37 3.28 1.47e+00 4.63e-01 4.98e+00 angle pdb=" N VAL R 82 " pdb=" CA VAL R 82 " pdb=" C VAL R 82 " ideal model delta sigma weight residual 112.76 110.13 2.63 1.27e+00 6.20e-01 4.30e+00 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5312 17.97 - 35.94: 179 35.94 - 53.92: 39 53.92 - 71.89: 4 71.89 - 89.86: 3 Dihedral angle restraints: 5537 sinusoidal: 2163 harmonic: 3374 Sorted by residual: dihedral pdb=" N PHE B 239 " pdb=" CA PHE B 239 " pdb=" CB PHE B 239 " pdb=" CG PHE B 239 " ideal model delta sinusoidal sigma weight residual -60.00 -118.25 58.25 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N ARG R 343 " pdb=" CA ARG R 343 " pdb=" CB ARG R 343 " pdb=" CG ARG R 343 " ideal model delta sinusoidal sigma weight residual -60.00 -114.86 54.86 3 1.50e+01 4.44e-03 9.31e+00 dihedral pdb=" N ARG E 191 " pdb=" CA ARG E 191 " pdb=" CB ARG E 191 " pdb=" CG ARG E 191 " ideal model delta sinusoidal sigma weight residual -180.00 -126.28 -53.72 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 5534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 927 0.028 - 0.057: 346 0.057 - 0.085: 82 0.085 - 0.114: 63 0.114 - 0.142: 22 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA VAL E 1 " pdb=" N VAL E 1 " pdb=" C VAL E 1 " pdb=" CB VAL E 1 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 1437 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 5 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO L 6 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO L 6 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 6 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 73 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL R 73 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL R 73 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY R 74 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP R 304 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO R 305 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 305 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 305 " -0.021 5.00e-02 4.00e+02 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 63 2.56 - 3.14: 7628 3.14 - 3.73: 13873 3.73 - 4.31: 19152 4.31 - 4.90: 32580 Nonbonded interactions: 73296 Sorted by model distance: nonbonded pdb=" O ARG A 35 " pdb=" OG1 THR A 219 " model vdw 1.974 3.040 nonbonded pdb=" O ASP B 338 " pdb=" OG SER B 339 " model vdw 2.205 3.040 nonbonded pdb=" NE2 GLN B 181 " pdb=" OG1 THR B 184 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASN A 359 " pdb=" OG SER R 341 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 232 " pdb=" OG SER B 250 " model vdw 2.233 3.040 ... (remaining 73291 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: 0.850 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.820 Find NCS groups from input model: 0.100 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 : 0.002 0.033 9349 Z= 0.131 Angle : 0.450 4.934 12690 Z= 0.256 Chirality : 0.038 0.142 1440 Planarity : 0.003 0.045 1611 Dihedral : 10.050 89.862 3359 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.20 % Allowed : 5.25 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1144 helix: 2.70 (0.28), residues: 382 sheet: 1.19 (0.32), residues: 263 loop : -0.37 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.002 0.000 HIS A 324 PHE 0.007 0.001 PHE R 97 TYR 0.007 0.001 TYR A 30 ARG 0.003 0.000 ARG R 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 340 ARG cc_start: 0.6653 (mmm160) cc_final: 0.6361 (tpp-160) REVERT: A 347 LYS cc_start: 0.7638 (ttpp) cc_final: 0.7116 (mtpp) REVERT: A 356 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.7268 (ttm110) REVERT: B 48 ILE cc_start: 0.7010 (mt) cc_final: 0.6676 (mt) REVERT: B 66 MET cc_start: 0.8277 (pp-130) cc_final: 0.7876 (pp-130) REVERT: B 217 ASP cc_start: 0.6937 (m-30) cc_final: 0.6620 (m-30) REVERT: B 244 ASN cc_start: 0.8002 (m-40) cc_final: 0.7760 (m-40) REVERT: B 298 ASN cc_start: 0.6343 (p0) cc_final: 0.6092 (p0) REVERT: B 340 PHE cc_start: 0.8186 (m-10) cc_final: 0.7981 (m-10) REVERT: E 79 PHE cc_start: 0.6927 (m-80) cc_final: 0.6660 (m-80) REVERT: E 166 LEU cc_start: 0.7979 (tt) cc_final: 0.7743 (tp) REVERT: G 23 ASN cc_start: 0.5707 (m-40) cc_final: 0.5481 (t0) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 1.1325 time to fit residues: 261.4629 Evaluate side-chains 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 204 GLN A 261 GLN A 324 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 181 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 179 GLN R 92 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9349 Z= 0.411 Angle : 0.749 9.805 12690 Z= 0.392 Chirality : 0.049 0.219 1440 Planarity : 0.006 0.071 1611 Dihedral : 4.945 22.518 1275 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.74 % Allowed : 12.71 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.75 (0.25), residues: 1144 helix: 1.68 (0.26), residues: 386 sheet: 0.73 (0.31), residues: 278 loop : -0.60 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 104 HIS 0.009 0.002 HIS E 34 PHE 0.027 0.003 PHE G 60 TYR 0.033 0.002 TYR B 269 ARG 0.009 0.001 ARG R 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.6314 (m-30) cc_final: 0.6103 (m-30) REVERT: A 340 ARG cc_start: 0.7100 (mmm160) cc_final: 0.6713 (tpp-160) REVERT: B 285 LYS cc_start: 0.7313 (mmtt) cc_final: 0.6824 (ptmm) REVERT: B 298 ASN cc_start: 0.7073 (p0) cc_final: 0.6856 (p0) REVERT: E 166 LEU cc_start: 0.8282 (tt) cc_final: 0.8052 (tp) REVERT: E 183 GLN cc_start: 0.6466 (mt0) cc_final: 0.6248 (mt0) REVERT: G 20 MET cc_start: 0.7059 (ptm) cc_final: 0.6740 (ptm) REVERT: R 125 ARG cc_start: 0.4675 (mtp-110) cc_final: 0.3927 (tmm-80) REVERT: R 253 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5443 (ttm110) REVERT: R 275 ARG cc_start: 0.5927 (ttt90) cc_final: 0.5684 (ttm-80) REVERT: R 315 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7105 (tm) outliers start: 47 outliers final: 21 residues processed: 187 average time/residue: 1.1434 time to fit residues: 229.5034 Evaluate side-chains 151 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 93 ASN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN R 101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9349 Z= 0.265 Angle : 0.601 8.934 12690 Z= 0.312 Chirality : 0.044 0.178 1440 Planarity : 0.004 0.045 1611 Dihedral : 4.588 20.961 1275 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.15 % Allowed : 14.73 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.25), residues: 1144 helix: 1.81 (0.26), residues: 390 sheet: 0.54 (0.31), residues: 279 loop : -0.62 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 104 HIS 0.005 0.001 HIS B 188 PHE 0.018 0.002 PHE G 60 TYR 0.016 0.002 TYR B 269 ARG 0.005 0.001 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6775 (tt0) REVERT: B 57 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7528 (mtt90) REVERT: B 122 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8347 (mp) REVERT: B 158 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: B 210 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7818 (p0) REVERT: B 222 MET cc_start: 0.7193 (ptp) cc_final: 0.6980 (pp-130) REVERT: B 285 LYS cc_start: 0.7365 (mmtt) cc_final: 0.6828 (ptmm) REVERT: E 166 LEU cc_start: 0.8232 (tt) cc_final: 0.7981 (tp) REVERT: E 183 GLN cc_start: 0.6717 (mt0) cc_final: 0.6461 (mt0) REVERT: R 167 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5422 (pp) REVERT: R 253 ARG cc_start: 0.5940 (OUTLIER) cc_final: 0.5420 (ttm110) REVERT: R 315 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7057 (tm) outliers start: 51 outliers final: 22 residues processed: 175 average time/residue: 1.1376 time to fit residues: 213.5965 Evaluate side-chains 162 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 329 HIS B 80 GLN B 181 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN R 317 GLN R 321 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9349 Z= 0.213 Angle : 0.574 8.549 12690 Z= 0.295 Chirality : 0.043 0.154 1440 Planarity : 0.004 0.044 1611 Dihedral : 4.468 19.796 1275 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.44 % Allowed : 16.25 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.25), residues: 1144 helix: 1.84 (0.26), residues: 392 sheet: 0.51 (0.31), residues: 266 loop : -0.61 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.008 0.001 HIS A 329 PHE 0.014 0.002 PHE R 297 TYR 0.013 0.001 TYR B 269 ARG 0.008 0.000 ARG R 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: B 158 ASP cc_start: 0.8289 (m-30) cc_final: 0.8077 (m-30) REVERT: B 222 MET cc_start: 0.7227 (ptp) cc_final: 0.7001 (pp-130) REVERT: B 285 LYS cc_start: 0.7295 (mmtt) cc_final: 0.6820 (ptmm) REVERT: B 308 ASP cc_start: 0.7836 (p0) cc_final: 0.7533 (p0) REVERT: E 166 LEU cc_start: 0.8220 (tt) cc_final: 0.7989 (tp) REVERT: E 183 GLN cc_start: 0.6743 (mt0) cc_final: 0.6448 (mt0) REVERT: G 20 MET cc_start: 0.6935 (ptm) cc_final: 0.6724 (ptm) REVERT: R 125 ARG cc_start: 0.4746 (mtp-110) cc_final: 0.4046 (mtp180) REVERT: R 167 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5278 (pp) REVERT: R 253 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5413 (ttm110) REVERT: R 315 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7139 (tm) outliers start: 44 outliers final: 23 residues processed: 165 average time/residue: 1.1424 time to fit residues: 202.3742 Evaluate side-chains 151 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 204 GLN A 213 GLN A 329 HIS B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 ASN R 317 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9349 Z= 0.192 Angle : 0.555 7.850 12690 Z= 0.284 Chirality : 0.043 0.172 1440 Planarity : 0.004 0.040 1611 Dihedral : 4.344 19.103 1275 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.54 % Allowed : 17.36 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.77 (0.25), residues: 1144 helix: 1.94 (0.26), residues: 391 sheet: 0.42 (0.31), residues: 276 loop : -0.61 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 87 HIS 0.008 0.001 HIS A 329 PHE 0.019 0.002 PHE E 67 TYR 0.010 0.001 TYR B 269 ARG 0.004 0.000 ARG R 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 188 LYS cc_start: 0.7400 (mttp) cc_final: 0.7148 (mmtm) REVERT: A 197 HIS cc_start: 0.7406 (m170) cc_final: 0.7056 (m90) REVERT: B 62 LYS cc_start: 0.8141 (pttp) cc_final: 0.7744 (pttp) REVERT: B 158 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: B 222 MET cc_start: 0.7273 (ptp) cc_final: 0.7038 (pp-130) REVERT: B 285 LYS cc_start: 0.7315 (mmtt) cc_final: 0.6834 (ptmm) REVERT: B 308 ASP cc_start: 0.7797 (p0) cc_final: 0.7525 (p0) REVERT: E 166 LEU cc_start: 0.8215 (tt) cc_final: 0.7981 (tp) REVERT: E 183 GLN cc_start: 0.6727 (mt0) cc_final: 0.6435 (mt0) REVERT: R 167 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5262 (pp) REVERT: R 253 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.5376 (ttm110) REVERT: R 315 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7091 (tm) outliers start: 45 outliers final: 25 residues processed: 165 average time/residue: 1.1784 time to fit residues: 208.9357 Evaluate side-chains 160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 329 HIS B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN R 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9349 Z= 0.219 Angle : 0.581 8.737 12690 Z= 0.298 Chirality : 0.043 0.172 1440 Planarity : 0.004 0.041 1611 Dihedral : 4.448 19.902 1275 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.24 % Allowed : 18.87 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.73 (0.25), residues: 1144 helix: 1.85 (0.26), residues: 391 sheet: 0.50 (0.32), residues: 266 loop : -0.64 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.008 0.001 HIS A 329 PHE 0.019 0.002 PHE R 297 TYR 0.011 0.001 TYR E 94 ARG 0.010 0.000 ARG R 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7555 (mtt90) REVERT: B 158 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: B 222 MET cc_start: 0.7319 (ptp) cc_final: 0.7119 (pp-130) REVERT: B 285 LYS cc_start: 0.7337 (mmtt) cc_final: 0.6834 (ptmm) REVERT: B 308 ASP cc_start: 0.7772 (p0) cc_final: 0.7531 (p0) REVERT: E 166 LEU cc_start: 0.8208 (tt) cc_final: 0.7995 (tp) REVERT: E 183 GLN cc_start: 0.6754 (mt0) cc_final: 0.6485 (mt0) REVERT: G 20 MET cc_start: 0.6875 (ptm) cc_final: 0.6611 (ptm) REVERT: R 125 ARG cc_start: 0.4834 (mtp-110) cc_final: 0.3904 (tmm-80) REVERT: R 167 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5536 (pp) REVERT: R 253 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5388 (ttm110) REVERT: R 315 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7075 (tm) outliers start: 42 outliers final: 23 residues processed: 158 average time/residue: 1.1486 time to fit residues: 194.8295 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0170 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 0.0070 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 329 HIS B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9349 Z= 0.159 Angle : 0.532 8.129 12690 Z= 0.274 Chirality : 0.042 0.161 1440 Planarity : 0.004 0.039 1611 Dihedral : 4.170 19.026 1275 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.23 % Allowed : 20.69 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.25), residues: 1144 helix: 2.02 (0.26), residues: 393 sheet: 0.52 (0.32), residues: 275 loop : -0.60 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 302 HIS 0.008 0.001 HIS A 329 PHE 0.021 0.001 PHE R 297 TYR 0.009 0.001 TYR E 94 ARG 0.007 0.000 ARG R 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7741 (mt) REVERT: B 158 ASP cc_start: 0.8247 (m-30) cc_final: 0.7918 (m-30) REVERT: B 285 LYS cc_start: 0.7308 (mmtt) cc_final: 0.6835 (ptmm) REVERT: B 308 ASP cc_start: 0.7733 (p0) cc_final: 0.7507 (p0) REVERT: E 166 LEU cc_start: 0.8181 (tt) cc_final: 0.7977 (tp) REVERT: E 183 GLN cc_start: 0.6723 (mt0) cc_final: 0.6422 (mt0) REVERT: R 125 ARG cc_start: 0.4883 (mtp-110) cc_final: 0.4004 (tmm-80) REVERT: R 167 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5267 (pp) REVERT: R 315 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7081 (tm) outliers start: 32 outliers final: 20 residues processed: 165 average time/residue: 1.2096 time to fit residues: 213.4232 Evaluate side-chains 163 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 204 GLN A 329 HIS B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9349 Z= 0.239 Angle : 0.595 9.349 12690 Z= 0.304 Chirality : 0.044 0.168 1440 Planarity : 0.004 0.041 1611 Dihedral : 4.456 20.032 1275 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.63 % Allowed : 21.09 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.25), residues: 1144 helix: 1.80 (0.26), residues: 393 sheet: 0.53 (0.32), residues: 266 loop : -0.64 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.008 0.001 HIS A 329 PHE 0.022 0.002 PHE R 297 TYR 0.011 0.001 TYR E 94 ARG 0.006 0.000 ARG R 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7813 (m-40) cc_final: 0.7467 (m-40) REVERT: A 197 HIS cc_start: 0.7365 (m170) cc_final: 0.7064 (m90) REVERT: B 57 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7622 (mtt90) REVERT: B 158 ASP cc_start: 0.8305 (m-30) cc_final: 0.8014 (m-30) REVERT: B 210 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7920 (p0) REVERT: B 285 LYS cc_start: 0.7374 (mmtt) cc_final: 0.6870 (ptmm) REVERT: B 308 ASP cc_start: 0.7795 (p0) cc_final: 0.7567 (p0) REVERT: E 166 LEU cc_start: 0.8197 (tt) cc_final: 0.7996 (tp) REVERT: E 183 GLN cc_start: 0.6824 (mt0) cc_final: 0.6521 (mt0) REVERT: R 315 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7080 (tm) outliers start: 36 outliers final: 21 residues processed: 159 average time/residue: 1.1381 time to fit residues: 194.4925 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 67 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS B 345 ASN R 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9349 Z= 0.276 Angle : 0.635 9.736 12690 Z= 0.325 Chirality : 0.045 0.168 1440 Planarity : 0.004 0.042 1611 Dihedral : 4.694 23.132 1275 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.63 % Allowed : 21.29 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.58 (0.25), residues: 1144 helix: 1.63 (0.26), residues: 389 sheet: 0.54 (0.32), residues: 260 loop : -0.68 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 104 HIS 0.008 0.001 HIS A 329 PHE 0.028 0.002 PHE R 297 TYR 0.012 0.002 TYR E 94 ARG 0.006 0.001 ARG R 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.997 Fit side-chains REVERT: A 195 ASN cc_start: 0.7906 (m-40) cc_final: 0.7601 (m-40) REVERT: B 62 LYS cc_start: 0.8056 (pttp) cc_final: 0.7720 (pttp) REVERT: B 158 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: B 210 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7957 (p0) REVERT: B 217 ASP cc_start: 0.7829 (m-30) cc_final: 0.7129 (t70) REVERT: B 285 LYS cc_start: 0.7349 (mmtt) cc_final: 0.6879 (ptmm) REVERT: B 308 ASP cc_start: 0.7806 (p0) cc_final: 0.7587 (p0) REVERT: E 166 LEU cc_start: 0.8233 (tt) cc_final: 0.8002 (tp) REVERT: E 183 GLN cc_start: 0.6883 (mt0) cc_final: 0.6605 (mt0) REVERT: R 315 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7065 (tm) outliers start: 36 outliers final: 24 residues processed: 156 average time/residue: 1.2041 time to fit residues: 201.5627 Evaluate side-chains 160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain R residue 334 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 204 GLN A 329 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9349 Z= 0.173 Angle : 0.576 9.048 12690 Z= 0.294 Chirality : 0.042 0.158 1440 Planarity : 0.004 0.040 1611 Dihedral : 4.338 19.368 1275 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.93 % Allowed : 22.00 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.67 (0.25), residues: 1144 helix: 1.80 (0.26), residues: 388 sheet: 0.48 (0.32), residues: 260 loop : -0.65 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 302 HIS 0.009 0.001 HIS A 197 PHE 0.032 0.002 PHE R 297 TYR 0.009 0.001 TYR A 306 ARG 0.005 0.000 ARG E 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7935 (m-40) cc_final: 0.7657 (m-40) REVERT: B 48 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7819 (mt) REVERT: B 57 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7485 (mtt180) REVERT: B 62 LYS cc_start: 0.7806 (pttp) cc_final: 0.6938 (pttt) REVERT: B 64 TYR cc_start: 0.7830 (m-80) cc_final: 0.7527 (m-80) REVERT: B 158 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: B 217 ASP cc_start: 0.7830 (m-30) cc_final: 0.7129 (t70) REVERT: B 285 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6815 (ptmm) REVERT: B 308 ASP cc_start: 0.7759 (p0) cc_final: 0.7551 (p0) REVERT: E 166 LEU cc_start: 0.8168 (tt) cc_final: 0.7943 (tp) REVERT: E 183 GLN cc_start: 0.6926 (mt0) cc_final: 0.6608 (mt0) REVERT: R 315 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7063 (tm) outliers start: 29 outliers final: 23 residues processed: 157 average time/residue: 1.1909 time to fit residues: 200.9728 Evaluate side-chains 162 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.193479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.157826 restraints weight = 9449.358| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.22 r_work: 0.3405 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9349 Z= 0.224 Angle : 0.611 9.401 12690 Z= 0.312 Chirality : 0.044 0.162 1440 Planarity : 0.004 0.042 1611 Dihedral : 4.494 20.010 1275 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.23 % Allowed : 22.00 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.60 (0.25), residues: 1144 helix: 1.70 (0.26), residues: 390 sheet: 0.52 (0.33), residues: 255 loop : -0.69 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.009 0.001 HIS A 197 PHE 0.035 0.002 PHE R 297 TYR 0.011 0.001 TYR E 94 ARG 0.006 0.000 ARG E 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3673.98 seconds wall clock time: 66 minutes 38.63 seconds (3998.63 seconds total)