Starting phenix.real_space_refine on Sun Apr 7 01:01:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/04_2024/8jit_36327_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/04_2024/8jit_36327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/04_2024/8jit_36327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/04_2024/8jit_36327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/04_2024/8jit_36327_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/04_2024/8jit_36327_neut_trim_updated.pdb" } resolution = 2.91 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= 0.020 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 56 5.16 5 C 5836 2.51 5 N 1617 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "P GLU 17": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 260": "OE1" <-> "OE2" Residue "R ASP 385": "OD1" <-> "OD2" Residue "R GLU 406": "OE1" <-> "OE2" Residue "R GLU 410": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9193 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1868 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 233 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2574 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3108 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.29, per 1000 atoms: 0.58 Number of scatterers: 9193 At special positions: 0 Unit cell: (77.112, 99.603, 175.644, 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 56 16.00 O 1684 8.00 N 1617 7.00 C 5836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.05 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 11 sheets defined 38.0% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 4 through 33 removed outlier: 3.806A pdb=" N ASN A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 215 through 221 removed outlier: 5.295A pdb=" N GLN A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N CYS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.869A pdb=" N GLU A 283 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 284 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.520A pdb=" N ARG A 301 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 335 Processing helix chain 'A' and resid 352 through 374 removed outlier: 3.504A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 28 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.755A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.525A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.855A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 29 through 48 Processing helix chain 'R' and resid 88 through 90 No H-bonds generated for 'chain 'R' and resid 88 through 90' Processing helix chain 'R' and resid 127 through 165 removed outlier: 3.557A pdb=" N LEU R 158 " --> pdb=" O GLY R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 202 removed outlier: 3.583A pdb=" N ASN R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 216 Processing helix chain 'R' and resid 221 through 254 removed outlier: 4.115A pdb=" N TYR R 239 " --> pdb=" O ILE R 235 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 271 Processing helix chain 'R' and resid 274 through 288 removed outlier: 3.686A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 305 through 316 Proline residue: R 310 - end of helix Processing helix chain 'R' and resid 319 through 333 Processing helix chain 'R' and resid 344 through 353 removed outlier: 3.837A pdb=" N THR R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU R 352 " --> pdb=" O ALA R 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 401 removed outlier: 4.355A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 420 removed outlier: 3.966A pdb=" N LEU R 420 " --> pdb=" O HIS R 416 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.983A pdb=" N VAL A 271 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N HIS A 346 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 273 " --> pdb=" O HIS A 346 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 227 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.712A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.061A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.909A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.965A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.993A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.803A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.644A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.582A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 75 through 80 415 hydrogen bonds defined for protein. 1194 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: 2.68 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1902 1.33 - 1.45: 2394 1.45 - 1.57: 5025 1.57 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9397 Sorted by residual: bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.341 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C04 D6M P 101 " pdb=" C09 D6M P 101 " ideal model delta sigma weight residual 1.550 1.486 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C THR A 309 " pdb=" N PRO A 310 " ideal model delta sigma weight residual 1.329 1.367 -0.037 1.22e-02 6.72e+03 9.28e+00 bond pdb=" CA THR N 111 " pdb=" C THR N 111 " ideal model delta sigma weight residual 1.529 1.487 0.042 1.40e-02 5.10e+03 9.01e+00 bond pdb=" CA CYS N 99 " pdb=" C CYS N 99 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.02e-02 9.61e+03 8.85e+00 ... (remaining 9392 not shown) Histogram of bond angle deviations from ideal: 96.92 - 105.00: 123 105.00 - 113.08: 5080 113.08 - 121.17: 5079 121.17 - 129.25: 2370 129.25 - 137.34: 91 Bond angle restraints: 12743 Sorted by residual: angle pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 118.04 96.92 21.12 3.00e+00 1.11e-01 4.96e+01 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 113.30 122.71 -9.41 1.34e+00 5.57e-01 4.93e+01 angle pdb=" C THR A 309 " pdb=" N PRO A 310 " pdb=" CA PRO A 310 " ideal model delta sigma weight residual 120.66 113.02 7.64 1.09e+00 8.42e-01 4.92e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.38 105.27 8.11 1.23e+00 6.61e-01 4.34e+01 angle pdb=" N TRP P 25 " pdb=" CA TRP P 25 " pdb=" C TRP P 25 " ideal model delta sigma weight residual 111.71 105.02 6.69 1.15e+00 7.56e-01 3.39e+01 ... (remaining 12738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5005 17.83 - 35.66: 430 35.66 - 53.48: 94 53.48 - 71.31: 23 71.31 - 89.14: 10 Dihedral angle restraints: 5562 sinusoidal: 2156 harmonic: 3406 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 -14.49 -71.51 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" N ASN C 59 " pdb=" C ASN C 59 " pdb=" CA ASN C 59 " pdb=" CB ASN C 59 " ideal model delta harmonic sigma weight residual 122.80 133.65 -10.85 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" C ASN C 59 " pdb=" N ASN C 59 " pdb=" CA ASN C 59 " pdb=" CB ASN C 59 " ideal model delta harmonic sigma weight residual -122.60 -132.44 9.84 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 5559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1319 0.095 - 0.191: 85 0.191 - 0.286: 7 0.286 - 0.381: 1 0.381 - 0.477: 2 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA ASN C 59 " pdb=" N ASN C 59 " pdb=" C ASN C 59 " pdb=" CB ASN C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CB VAL R 212 " pdb=" CA VAL R 212 " pdb=" CG1 VAL R 212 " pdb=" CG2 VAL R 212 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1411 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER N 25 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C SER N 25 " -0.049 2.00e-02 2.50e+03 pdb=" O SER N 25 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY N 26 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 355 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO R 356 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 356 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 356 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 274 " 0.035 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO R 275 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " 0.030 5.00e-02 4.00e+02 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1117 2.74 - 3.28: 9605 3.28 - 3.82: 15700 3.82 - 4.36: 18162 4.36 - 4.90: 30834 Nonbonded interactions: 75418 Sorted by model distance: nonbonded pdb=" O ALA R 175 " pdb=" ND2 ASN R 179 " model vdw 2.204 2.520 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.223 2.440 nonbonded pdb=" O TYR A 302 " pdb=" NH2 ARG A 320 " model vdw 2.260 2.520 nonbonded pdb=" O ARG B 22 " pdb=" NH1 ARG B 22 " model vdw 2.263 2.520 nonbonded pdb=" OE1 GLN P 3 " pdb=" OH TYR R 149 " model vdw 2.269 2.440 ... (remaining 75413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 3.890 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.950 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 0.094 9397 Z= 0.359 Angle : 0.786 21.123 12743 Z= 0.498 Chirality : 0.052 0.477 1414 Planarity : 0.004 0.065 1634 Dihedral : 14.715 89.141 3342 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 30.83 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.52 % Favored : 93.97 % Rotamer: Outliers : 4.69 % Allowed : 3.34 % Favored : 91.97 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1160 helix: 1.12 (0.27), residues: 429 sheet: -0.78 (0.35), residues: 232 loop : -1.33 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 36 HIS 0.005 0.001 HIS R 44 PHE 0.024 0.001 PHE B 253 TYR 0.015 0.001 TYR N 115 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 188 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 THR cc_start: 0.5987 (t) cc_final: 0.5655 (t) REVERT: A 278 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: B 17 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8795 (pp30) REVERT: B 188 MET cc_start: 0.8680 (mmm) cc_final: 0.8290 (mmm) REVERT: B 254 ASP cc_start: 0.8054 (t70) cc_final: 0.7834 (t0) REVERT: C 13 ARG cc_start: 0.9337 (ttm110) cc_final: 0.9136 (ttm110) REVERT: C 42 GLU cc_start: 0.8809 (pp20) cc_final: 0.8443 (pp20) REVERT: N 2 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8200 (p) REVERT: R 34 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8753 (tm-30) REVERT: R 142 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8161 (mt0) REVERT: R 354 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8546 (tt) REVERT: R 362 GLU cc_start: 0.8769 (tp30) cc_final: 0.8552 (tp30) REVERT: R 407 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8825 (p) outliers start: 45 outliers final: 7 residues processed: 217 average time/residue: 1.3702 time to fit residues: 315.5818 Evaluate side-chains 139 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 142 GLN Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 340 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 GLN R 177 HIS R 179 ASN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 GLN ** R 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9397 Z= 0.243 Angle : 0.632 10.040 12743 Z= 0.323 Chirality : 0.042 0.209 1414 Planarity : 0.004 0.062 1634 Dihedral : 6.692 83.461 1324 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.14 % Favored : 95.60 % Rotamer: Outliers : 2.82 % Allowed : 14.29 % Favored : 82.90 % 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: -0.05 (0.25), residues: 1160 helix: 1.65 (0.26), residues: 434 sheet: -0.65 (0.34), residues: 234 loop : -1.25 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 36 HIS 0.006 0.001 HIS R 177 PHE 0.019 0.001 PHE P 6 TYR 0.025 0.002 TYR R 145 ARG 0.006 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8557 (mt-10) REVERT: A 278 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: B 8 ARG cc_start: 0.9475 (mtp180) cc_final: 0.8918 (mtt180) REVERT: B 15 LYS cc_start: 0.9391 (tttt) cc_final: 0.9007 (tmmt) REVERT: B 158 VAL cc_start: 0.9325 (t) cc_final: 0.9013 (p) REVERT: B 188 MET cc_start: 0.9003 (mmm) cc_final: 0.8673 (mmm) REVERT: B 260 GLU cc_start: 0.8282 (pt0) cc_final: 0.7906 (tt0) REVERT: B 262 MET cc_start: 0.7860 (tpt) cc_final: 0.7453 (tpp) REVERT: B 298 ASP cc_start: 0.8413 (t0) cc_final: 0.8069 (t0) REVERT: B 301 LYS cc_start: 0.7781 (mmpt) cc_final: 0.7420 (mmmt) REVERT: C 13 ARG cc_start: 0.9294 (ttm110) cc_final: 0.9020 (ttm110) REVERT: C 17 GLU cc_start: 0.8870 (tp30) cc_final: 0.8570 (mp0) REVERT: C 42 GLU cc_start: 0.8708 (pp20) cc_final: 0.8380 (pp20) REVERT: C 58 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8804 (mt-10) REVERT: N 87 LYS cc_start: 0.8756 (tppp) cc_final: 0.8392 (ttmp) REVERT: R 34 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8785 (tm-30) REVERT: R 290 GLU cc_start: 0.6634 (pp20) cc_final: 0.6417 (pp20) REVERT: R 410 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8595 (tm-30) outliers start: 27 outliers final: 15 residues processed: 164 average time/residue: 1.3363 time to fit residues: 233.7007 Evaluate side-chains 152 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 133 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN R 392 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9397 Z= 0.301 Angle : 0.617 12.716 12743 Z= 0.317 Chirality : 0.042 0.148 1414 Planarity : 0.004 0.073 1634 Dihedral : 6.030 73.915 1308 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 3.96 % Allowed : 16.68 % Favored : 79.35 % 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: 0.05 (0.25), residues: 1160 helix: 1.66 (0.26), residues: 433 sheet: -0.55 (0.33), residues: 236 loop : -1.14 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 36 HIS 0.006 0.001 HIS R 361 PHE 0.019 0.002 PHE P 6 TYR 0.024 0.002 TYR R 145 ARG 0.005 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 1.289 Fit side-chains REVERT: A 21 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8573 (mm-30) REVERT: P 17 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8443 (tp30) REVERT: B 8 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.9003 (mtt180) REVERT: B 15 LYS cc_start: 0.9432 (tttt) cc_final: 0.9069 (tmmt) REVERT: B 17 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8836 (pp30) REVERT: B 158 VAL cc_start: 0.9264 (t) cc_final: 0.8928 (p) REVERT: B 188 MET cc_start: 0.8966 (mmm) cc_final: 0.8599 (mmm) REVERT: B 260 GLU cc_start: 0.8458 (pt0) cc_final: 0.8086 (tt0) REVERT: C 13 ARG cc_start: 0.9274 (ttm110) cc_final: 0.9065 (ttm110) REVERT: C 42 GLU cc_start: 0.8787 (pp20) cc_final: 0.8417 (pp20) REVERT: C 58 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8837 (mt-10) REVERT: N 87 LYS cc_start: 0.8889 (tppp) cc_final: 0.8638 (ttmp) REVERT: N 89 GLU cc_start: 0.8630 (pm20) cc_final: 0.8373 (pm20) REVERT: R 34 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8797 (tm-30) REVERT: R 115 TRP cc_start: 0.8540 (m100) cc_final: 0.8320 (m100) REVERT: R 290 GLU cc_start: 0.6781 (pp20) cc_final: 0.6570 (pp20) REVERT: R 410 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8615 (tm-30) outliers start: 38 outliers final: 21 residues processed: 157 average time/residue: 1.2905 time to fit residues: 216.0753 Evaluate side-chains 147 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN N 82 GLN R 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9397 Z= 0.243 Angle : 0.580 9.376 12743 Z= 0.297 Chirality : 0.041 0.144 1414 Planarity : 0.004 0.077 1634 Dihedral : 5.433 56.356 1304 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.60 % Rotamer: Outliers : 4.80 % Allowed : 18.77 % Favored : 76.43 % 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: 0.20 (0.26), residues: 1160 helix: 1.78 (0.26), residues: 438 sheet: -0.46 (0.33), residues: 235 loop : -1.08 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP N 36 HIS 0.005 0.001 HIS R 361 PHE 0.017 0.001 PHE P 6 TYR 0.021 0.002 TYR R 145 ARG 0.008 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8528 (mm-30) REVERT: A 213 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8411 (p0) REVERT: P 17 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8470 (tp30) REVERT: B 15 LYS cc_start: 0.9441 (tttt) cc_final: 0.9111 (tmmt) REVERT: B 188 MET cc_start: 0.8995 (mmm) cc_final: 0.8626 (mmm) REVERT: B 217 MET cc_start: 0.7172 (pmm) cc_final: 0.6835 (pmm) REVERT: B 260 GLU cc_start: 0.8510 (pt0) cc_final: 0.8165 (tt0) REVERT: C 13 ARG cc_start: 0.9291 (ttm110) cc_final: 0.9007 (ttm110) REVERT: C 17 GLU cc_start: 0.9031 (tp30) cc_final: 0.8597 (mp0) REVERT: C 29 LYS cc_start: 0.8920 (tppp) cc_final: 0.8718 (tppp) REVERT: C 42 GLU cc_start: 0.8774 (pp20) cc_final: 0.8390 (pp20) REVERT: C 58 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8802 (mt-10) REVERT: N 38 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8490 (ptp90) REVERT: N 46 GLU cc_start: 0.7904 (pt0) cc_final: 0.7570 (pt0) REVERT: N 87 LYS cc_start: 0.8837 (tppp) cc_final: 0.8556 (ttmm) REVERT: N 89 GLU cc_start: 0.8596 (pm20) cc_final: 0.8314 (pm20) REVERT: R 34 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8799 (tm-30) REVERT: R 50 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8364 (tp) REVERT: R 115 TRP cc_start: 0.8508 (m100) cc_final: 0.8286 (m100) REVERT: R 290 GLU cc_start: 0.6803 (pp20) cc_final: 0.6298 (pp20) REVERT: R 349 LYS cc_start: 0.6128 (mptt) cc_final: 0.5856 (mptt) REVERT: R 406 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8349 (tm-30) REVERT: R 410 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8546 (tm-30) outliers start: 46 outliers final: 24 residues processed: 163 average time/residue: 1.2591 time to fit residues: 219.2027 Evaluate side-chains 153 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 overall best weight: 1.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9397 Z= 0.283 Angle : 0.603 10.554 12743 Z= 0.309 Chirality : 0.042 0.151 1414 Planarity : 0.004 0.073 1634 Dihedral : 5.509 58.531 1304 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.14 % Favored : 95.69 % Rotamer: Outliers : 5.01 % Allowed : 19.71 % Favored : 75.29 % 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: 0.27 (0.26), residues: 1160 helix: 1.79 (0.26), residues: 436 sheet: -0.40 (0.33), residues: 238 loop : -0.98 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP N 36 HIS 0.005 0.001 HIS R 361 PHE 0.017 0.001 PHE P 6 TYR 0.022 0.002 TYR R 145 ARG 0.011 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 138 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8462 (mm-30) REVERT: A 213 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8452 (p0) REVERT: P 17 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8446 (tp30) REVERT: B 15 LYS cc_start: 0.9453 (tttt) cc_final: 0.9183 (tmmt) REVERT: B 22 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8538 (tpp-160) REVERT: B 34 THR cc_start: 0.8257 (p) cc_final: 0.8023 (p) REVERT: B 59 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8620 (t80) REVERT: B 158 VAL cc_start: 0.9361 (t) cc_final: 0.9067 (p) REVERT: B 188 MET cc_start: 0.8951 (mmm) cc_final: 0.8574 (mmm) REVERT: B 217 MET cc_start: 0.7429 (pmm) cc_final: 0.7181 (pmm) REVERT: B 260 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: C 13 ARG cc_start: 0.9305 (ttm110) cc_final: 0.9068 (ttm110) REVERT: C 21 MET cc_start: 0.8250 (mpp) cc_final: 0.7904 (mpp) REVERT: C 42 GLU cc_start: 0.8786 (pp20) cc_final: 0.8380 (pp20) REVERT: C 58 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8663 (mt-10) REVERT: N 87 LYS cc_start: 0.8925 (tppp) cc_final: 0.8549 (ttmm) REVERT: N 89 GLU cc_start: 0.8617 (pm20) cc_final: 0.8248 (pm20) REVERT: R 34 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8802 (tm-30) REVERT: R 50 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8355 (tp) REVERT: R 127 GLU cc_start: 0.7228 (mp0) cc_final: 0.6870 (mp0) REVERT: R 290 GLU cc_start: 0.6822 (pp20) cc_final: 0.6214 (pp20) REVERT: R 406 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8353 (tm-30) REVERT: R 410 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8433 (tm-30) outliers start: 48 outliers final: 27 residues processed: 166 average time/residue: 1.2336 time to fit residues: 219.6979 Evaluate side-chains 167 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 126 GLU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9397 Z= 0.198 Angle : 0.598 12.335 12743 Z= 0.299 Chirality : 0.040 0.204 1414 Planarity : 0.004 0.078 1634 Dihedral : 5.272 57.664 1304 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 3.96 % Allowed : 21.58 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1160 helix: 1.90 (0.26), residues: 438 sheet: -0.32 (0.33), residues: 235 loop : -0.95 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 36 HIS 0.005 0.001 HIS R 361 PHE 0.015 0.001 PHE P 6 TYR 0.020 0.001 TYR R 145 ARG 0.010 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 0.975 Fit side-chains REVERT: A 21 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8377 (mt-10) REVERT: P 17 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8442 (tp30) REVERT: B 15 LYS cc_start: 0.9417 (tttt) cc_final: 0.9164 (tmmt) REVERT: B 22 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8517 (tpp-160) REVERT: B 59 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.8634 (t80) REVERT: B 158 VAL cc_start: 0.9324 (t) cc_final: 0.9050 (p) REVERT: B 188 MET cc_start: 0.8949 (mmm) cc_final: 0.8562 (mmm) REVERT: B 217 MET cc_start: 0.7505 (pmm) cc_final: 0.7248 (pmm) REVERT: B 260 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: B 291 ASP cc_start: 0.8460 (m-30) cc_final: 0.8187 (m-30) REVERT: C 13 ARG cc_start: 0.9301 (ttm110) cc_final: 0.9013 (ttm110) REVERT: C 17 GLU cc_start: 0.9033 (tp30) cc_final: 0.8544 (mp0) REVERT: C 42 GLU cc_start: 0.8744 (pp20) cc_final: 0.8333 (pp20) REVERT: C 58 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8696 (mt-10) REVERT: N 38 ARG cc_start: 0.8857 (ptt180) cc_final: 0.8579 (ptt180) REVERT: N 87 LYS cc_start: 0.8911 (tppp) cc_final: 0.8514 (ttmm) REVERT: N 89 GLU cc_start: 0.8620 (pm20) cc_final: 0.8234 (pm20) REVERT: R 34 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8789 (tm-30) REVERT: R 50 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8379 (tp) REVERT: R 115 TRP cc_start: 0.8459 (m100) cc_final: 0.8157 (m100) REVERT: R 290 GLU cc_start: 0.7024 (pp20) cc_final: 0.6446 (pp20) REVERT: R 349 LYS cc_start: 0.6098 (mptt) cc_final: 0.5747 (mptt) REVERT: R 406 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8358 (tm-30) REVERT: R 410 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8471 (tm-30) outliers start: 38 outliers final: 23 residues processed: 164 average time/residue: 1.2733 time to fit residues: 224.0929 Evaluate side-chains 159 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9397 Z= 0.205 Angle : 0.601 12.377 12743 Z= 0.301 Chirality : 0.040 0.144 1414 Planarity : 0.004 0.077 1634 Dihedral : 5.155 57.755 1302 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.14 % Favored : 95.69 % Rotamer: Outliers : 4.38 % Allowed : 21.58 % Favored : 74.04 % 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: 0.42 (0.26), residues: 1160 helix: 1.88 (0.26), residues: 443 sheet: -0.25 (0.33), residues: 234 loop : -0.95 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP N 36 HIS 0.005 0.001 HIS R 361 PHE 0.014 0.001 PHE R 303 TYR 0.020 0.001 TYR R 145 ARG 0.012 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8382 (mt-10) REVERT: A 213 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8514 (p0) REVERT: P 17 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8450 (tp30) REVERT: B 15 LYS cc_start: 0.9429 (tttt) cc_final: 0.9191 (tmmt) REVERT: B 22 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8527 (tpp-160) REVERT: B 59 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8774 (t80) REVERT: B 158 VAL cc_start: 0.9327 (t) cc_final: 0.9056 (p) REVERT: B 188 MET cc_start: 0.8961 (mmm) cc_final: 0.8699 (mmm) REVERT: B 217 MET cc_start: 0.7569 (pmm) cc_final: 0.7273 (pmm) REVERT: B 260 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: B 291 ASP cc_start: 0.8450 (m-30) cc_final: 0.8184 (m-30) REVERT: C 13 ARG cc_start: 0.9293 (ttm110) cc_final: 0.9064 (ttm110) REVERT: C 21 MET cc_start: 0.7927 (mpp) cc_final: 0.7632 (mpp) REVERT: C 42 GLU cc_start: 0.8739 (pp20) cc_final: 0.8322 (pp20) REVERT: C 58 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8718 (mt-10) REVERT: N 38 ARG cc_start: 0.8907 (ptt180) cc_final: 0.8706 (ptt180) REVERT: N 87 LYS cc_start: 0.8914 (tppp) cc_final: 0.8578 (ttmm) REVERT: N 89 GLU cc_start: 0.8627 (pm20) cc_final: 0.8317 (pm20) REVERT: R 34 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8794 (tm-30) REVERT: R 50 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8304 (tp) REVERT: R 115 TRP cc_start: 0.8496 (m100) cc_final: 0.8195 (m100) REVERT: R 133 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: R 290 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6498 (pp20) REVERT: R 349 LYS cc_start: 0.6116 (mptt) cc_final: 0.5739 (mptt) outliers start: 42 outliers final: 26 residues processed: 157 average time/residue: 1.2648 time to fit residues: 212.6735 Evaluate side-chains 165 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9397 Z= 0.184 Angle : 0.622 12.454 12743 Z= 0.304 Chirality : 0.040 0.176 1414 Planarity : 0.004 0.073 1634 Dihedral : 5.015 57.503 1302 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 4.07 % Allowed : 22.73 % Favored : 73.20 % 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 (0.26), residues: 1160 helix: 1.99 (0.26), residues: 443 sheet: -0.22 (0.33), residues: 234 loop : -0.89 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP N 36 HIS 0.005 0.001 HIS R 361 PHE 0.014 0.001 PHE R 303 TYR 0.020 0.001 TYR R 145 ARG 0.013 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8386 (mt-10) REVERT: P 17 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8450 (tp30) REVERT: P 27 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8199 (mm-30) REVERT: B 15 LYS cc_start: 0.9444 (tttt) cc_final: 0.9214 (tmmt) REVERT: B 22 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8561 (tpp-160) REVERT: B 59 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8753 (t80) REVERT: B 158 VAL cc_start: 0.9322 (t) cc_final: 0.9053 (p) REVERT: B 188 MET cc_start: 0.8952 (mmm) cc_final: 0.8613 (mmm) REVERT: B 217 MET cc_start: 0.7582 (pmm) cc_final: 0.7189 (pmm) REVERT: B 260 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: B 262 MET cc_start: 0.7846 (tpt) cc_final: 0.7485 (tpp) REVERT: B 273 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9019 (mp) REVERT: B 291 ASP cc_start: 0.8414 (m-30) cc_final: 0.8170 (m-30) REVERT: C 13 ARG cc_start: 0.9295 (ttm110) cc_final: 0.9072 (ttm110) REVERT: C 21 MET cc_start: 0.7900 (mpp) cc_final: 0.7532 (mpp) REVERT: C 42 GLU cc_start: 0.8715 (pp20) cc_final: 0.8299 (pp20) REVERT: C 58 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8726 (mt-10) REVERT: N 87 LYS cc_start: 0.8909 (tppp) cc_final: 0.8514 (ttmm) REVERT: N 89 GLU cc_start: 0.8621 (pm20) cc_final: 0.8285 (pm20) REVERT: R 34 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8821 (tm-30) REVERT: R 50 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8227 (tp) REVERT: R 115 TRP cc_start: 0.8526 (m100) cc_final: 0.8211 (m100) REVERT: R 127 GLU cc_start: 0.7177 (mp0) cc_final: 0.6959 (mp0) REVERT: R 290 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6522 (pp20) REVERT: R 349 LYS cc_start: 0.6032 (mptt) cc_final: 0.5716 (mptt) REVERT: R 410 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8479 (tm-30) outliers start: 39 outliers final: 27 residues processed: 161 average time/residue: 1.1983 time to fit residues: 206.7615 Evaluate side-chains 167 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 61 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9397 Z= 0.174 Angle : 0.624 12.637 12743 Z= 0.305 Chirality : 0.040 0.143 1414 Planarity : 0.004 0.074 1634 Dihedral : 4.856 56.983 1302 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 3.44 % Allowed : 23.77 % Favored : 72.78 % 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: 0.62 (0.26), residues: 1160 helix: 2.02 (0.26), residues: 443 sheet: -0.14 (0.34), residues: 234 loop : -0.82 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP N 36 HIS 0.004 0.001 HIS R 361 PHE 0.014 0.001 PHE R 33 TYR 0.020 0.001 TYR R 145 ARG 0.014 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8391 (mt-10) REVERT: A 213 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8524 (p0) REVERT: P 17 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8507 (tp30) REVERT: B 15 LYS cc_start: 0.9448 (tttt) cc_final: 0.9219 (tmmt) REVERT: B 22 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8301 (tpp-160) REVERT: B 34 THR cc_start: 0.8630 (p) cc_final: 0.8429 (t) REVERT: B 158 VAL cc_start: 0.9306 (t) cc_final: 0.9052 (p) REVERT: B 188 MET cc_start: 0.8970 (mmm) cc_final: 0.8608 (mmm) REVERT: B 217 MET cc_start: 0.7679 (pmm) cc_final: 0.7269 (pmm) REVERT: B 262 MET cc_start: 0.7837 (tpt) cc_final: 0.7472 (tpp) REVERT: B 273 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.9016 (mp) REVERT: C 13 ARG cc_start: 0.9295 (ttm110) cc_final: 0.9087 (ttm110) REVERT: C 42 GLU cc_start: 0.8712 (pp20) cc_final: 0.8337 (pp20) REVERT: C 58 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8729 (mt-10) REVERT: N 43 LYS cc_start: 0.7838 (mppt) cc_final: 0.7495 (mppt) REVERT: N 87 LYS cc_start: 0.8902 (tppp) cc_final: 0.8461 (ttmm) REVERT: N 89 GLU cc_start: 0.8609 (pm20) cc_final: 0.8197 (pm20) REVERT: R 34 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8798 (tm-30) REVERT: R 50 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8062 (tp) REVERT: R 115 TRP cc_start: 0.8512 (m100) cc_final: 0.8215 (m100) REVERT: R 123 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8112 (tpp) REVERT: R 127 GLU cc_start: 0.7144 (mp0) cc_final: 0.6543 (mp0) REVERT: R 290 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6549 (pp20) REVERT: R 349 LYS cc_start: 0.6032 (mptt) cc_final: 0.5717 (mptt) REVERT: R 410 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8484 (tm-30) outliers start: 33 outliers final: 22 residues processed: 160 average time/residue: 1.1969 time to fit residues: 205.4693 Evaluate side-chains 159 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 126 GLU Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9397 Z= 0.231 Angle : 0.643 12.312 12743 Z= 0.314 Chirality : 0.041 0.159 1414 Planarity : 0.004 0.073 1634 Dihedral : 4.963 58.020 1302 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 3.34 % Allowed : 24.82 % Favored : 71.85 % 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: 0.63 (0.26), residues: 1160 helix: 2.03 (0.26), residues: 443 sheet: -0.11 (0.33), residues: 234 loop : -0.83 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP N 36 HIS 0.005 0.001 HIS R 361 PHE 0.016 0.001 PHE R 230 TYR 0.022 0.001 TYR R 145 ARG 0.015 0.000 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8391 (mt-10) REVERT: A 213 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8516 (p0) REVERT: A 280 LEU cc_start: 0.9245 (tm) cc_final: 0.8483 (tm) REVERT: P 17 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8513 (tp30) REVERT: B 15 LYS cc_start: 0.9453 (tttt) cc_final: 0.9220 (tmmt) REVERT: B 22 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8591 (tpp-160) REVERT: B 34 THR cc_start: 0.8640 (p) cc_final: 0.8436 (t) REVERT: B 158 VAL cc_start: 0.9305 (t) cc_final: 0.9042 (p) REVERT: B 188 MET cc_start: 0.8977 (mmm) cc_final: 0.8641 (mmm) REVERT: B 217 MET cc_start: 0.7684 (pmm) cc_final: 0.7262 (pmm) REVERT: B 273 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8952 (mp) REVERT: C 13 ARG cc_start: 0.9330 (ttm110) cc_final: 0.9118 (ttm110) REVERT: C 42 GLU cc_start: 0.8719 (pp20) cc_final: 0.8285 (pp20) REVERT: C 58 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8722 (mt-10) REVERT: N 87 LYS cc_start: 0.8936 (tppp) cc_final: 0.8519 (ttmm) REVERT: N 89 GLU cc_start: 0.8617 (pm20) cc_final: 0.8246 (pm20) REVERT: R 34 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8770 (tm-30) REVERT: R 50 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7997 (tp) REVERT: R 115 TRP cc_start: 0.8506 (m100) cc_final: 0.8215 (m100) REVERT: R 123 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8125 (tpp) REVERT: R 290 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6441 (pp20) REVERT: R 349 LYS cc_start: 0.6077 (mptt) cc_final: 0.5733 (mptt) outliers start: 32 outliers final: 24 residues processed: 152 average time/residue: 1.2147 time to fit residues: 197.7895 Evaluate side-chains 168 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.068143 restraints weight = 19397.202| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.38 r_work: 0.2880 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9397 Z= 0.235 Angle : 0.662 12.291 12743 Z= 0.322 Chirality : 0.041 0.149 1414 Planarity : 0.004 0.075 1634 Dihedral : 5.073 59.360 1302 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.34 % Rotamer: Outliers : 3.75 % Allowed : 24.50 % Favored : 71.74 % 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: 0.66 (0.26), residues: 1160 helix: 2.01 (0.26), residues: 443 sheet: -0.18 (0.33), residues: 244 loop : -0.71 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP N 36 HIS 0.005 0.001 HIS R 361 PHE 0.016 0.001 PHE R 230 TYR 0.021 0.001 TYR R 145 ARG 0.014 0.000 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3875.02 seconds wall clock time: 69 minutes 51.68 seconds (4191.68 seconds total)