Starting phenix.real_space_refine on Tue Nov 14 18:14:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/11_2023/8jit_36327_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/11_2023/8jit_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_36327/11_2023/8jit_36327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/11_2023/8jit_36327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/11_2023/8jit_36327_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jit_36327/11_2023/8jit_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 5.17, per 1000 atoms: 0.56 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: 3.53 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: 1.69 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: 2.53 Time building geometry restraints manager: 3.78 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: 5003 17.83 - 35.66: 429 35.66 - 53.48: 89 53.48 - 71.31: 23 71.31 - 89.14: 10 Dihedral angle restraints: 5554 sinusoidal: 2148 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 5551 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: 1.040 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: 3.970 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.290 Find NCS groups from input model: 0.250 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- 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 : 14.611 89.141 3334 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 *********************** 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 : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 7 residues processed: 217 average time/residue: 1.3161 time to fit residues: 303.0237 Evaluate side-chains 127 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 2.0171 time to fit residues: 3.3636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 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: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 337 GLN R 392 GLN R 408 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9397 Z= 0.246 Angle : 0.647 11.153 12743 Z= 0.328 Chirality : 0.043 0.214 1414 Planarity : 0.004 0.064 1634 Dihedral : 4.804 49.332 1293 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 3.02 % Allowed : 13.87 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1160 helix: 1.69 (0.26), residues: 433 sheet: -0.64 (0.34), residues: 234 loop : -1.24 (0.28), residues: 493 *********************** 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: 29 poor density : 150 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 166 average time/residue: 1.2328 time to fit residues: 218.6591 Evaluate side-chains 146 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.3076 time to fit residues: 4.4697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN R 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9397 Z= 0.198 Angle : 0.605 12.282 12743 Z= 0.305 Chirality : 0.041 0.153 1414 Planarity : 0.004 0.071 1634 Dihedral : 4.810 55.781 1293 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.29 % Rotamer: Outliers : 3.55 % Allowed : 16.58 % Favored : 79.87 % 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: 0.15 (0.26), residues: 1160 helix: 1.75 (0.26), residues: 433 sheet: -0.40 (0.34), residues: 235 loop : -1.14 (0.28), residues: 492 *********************** 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 181 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.108 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 167 average time/residue: 1.2233 time to fit residues: 218.5933 Evaluate side-chains 145 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 6 average time/residue: 0.1181 time to fit residues: 2.6908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0670 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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 R 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9397 Z= 0.226 Angle : 0.606 11.163 12743 Z= 0.306 Chirality : 0.041 0.143 1414 Planarity : 0.004 0.073 1634 Dihedral : 4.917 59.278 1293 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.14 % Favored : 95.69 % Rotamer: Outliers : 4.59 % Allowed : 18.77 % Favored : 76.64 % 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: 433 sheet: -0.34 (0.34), residues: 242 loop : -1.01 (0.28), residues: 485 *********************** 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 171 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 1.059 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 156 average time/residue: 1.2156 time to fit residues: 203.0733 Evaluate side-chains 146 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 9 average time/residue: 0.3314 time to fit residues: 5.0774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 R 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9397 Z= 0.290 Angle : 0.633 11.023 12743 Z= 0.321 Chirality : 0.042 0.147 1414 Planarity : 0.004 0.076 1634 Dihedral : 5.112 57.236 1293 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 4.48 % Allowed : 20.23 % 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: 0.28 (0.25), residues: 1160 helix: 1.79 (0.26), residues: 436 sheet: -0.31 (0.34), residues: 241 loop : -1.02 (0.28), residues: 483 *********************** 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 169 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 126 time to evaluate : 1.190 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 27 residues processed: 152 average time/residue: 1.1688 time to fit residues: 191.0761 Evaluate side-chains 148 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 9 average time/residue: 0.2805 time to fit residues: 4.6016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN R 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9397 Z= 0.261 Angle : 0.617 11.201 12743 Z= 0.315 Chirality : 0.041 0.145 1414 Planarity : 0.004 0.076 1634 Dihedral : 5.100 57.064 1293 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 4.38 % Allowed : 21.38 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1160 helix: 1.74 (0.25), residues: 438 sheet: -0.28 (0.33), residues: 245 loop : -0.97 (0.29), residues: 477 *********************** 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 173 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.056 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 31 residues processed: 158 average time/residue: 1.1518 time to fit residues: 195.8937 Evaluate side-chains 151 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 21 residues processed: 11 average time/residue: 0.3074 time to fit residues: 5.5964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 0.0000 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 R 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3352 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= 0.208 Angle : 0.634 11.404 12743 Z= 0.319 Chirality : 0.040 0.143 1414 Planarity : 0.004 0.076 1634 Dihedral : 4.964 55.460 1293 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 4.28 % Allowed : 22.11 % Favored : 73.62 % 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: 0.40 (0.26), residues: 1160 helix: 1.84 (0.25), residues: 437 sheet: -0.21 (0.34), residues: 240 loop : -0.93 (0.29), residues: 483 *********************** 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 178 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 1.187 Fit side-chains outliers start: 41 outliers final: 26 residues processed: 162 average time/residue: 1.2669 time to fit residues: 220.7027 Evaluate side-chains 148 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 0.3558 time to fit residues: 4.0444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN R 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3442 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= 0.206 Angle : 0.673 11.422 12743 Z= 0.332 Chirality : 0.041 0.177 1414 Planarity : 0.004 0.074 1634 Dihedral : 4.912 53.589 1293 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.26 % Rotamer: Outliers : 3.44 % Allowed : 23.67 % Favored : 72.89 % 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: 0.48 (0.26), residues: 1160 helix: 1.92 (0.25), residues: 437 sheet: -0.19 (0.33), residues: 240 loop : -0.88 (0.29), residues: 483 *********************** 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 161 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 1.100 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 150 average time/residue: 1.1866 time to fit residues: 191.2900 Evaluate side-chains 149 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.5340 time to fit residues: 6.5032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0270 chunk 104 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 0.5416 ------------------------------------------------------------------------------- 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: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9397 Z= 0.201 Angle : 0.690 12.062 12743 Z= 0.339 Chirality : 0.041 0.210 1414 Planarity : 0.004 0.074 1634 Dihedral : 4.837 52.190 1293 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 2.92 % Allowed : 24.82 % Favored : 72.26 % 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: 0.50 (0.26), residues: 1160 helix: 1.86 (0.25), residues: 443 sheet: -0.10 (0.33), residues: 239 loop : -0.88 (0.29), residues: 478 *********************** 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 156 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 25 residues processed: 150 average time/residue: 1.2103 time to fit residues: 194.8100 Evaluate side-chains 146 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 5 average time/residue: 0.5093 time to fit residues: 4.3270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9397 Z= 0.217 Angle : 0.733 12.680 12743 Z= 0.358 Chirality : 0.041 0.188 1414 Planarity : 0.004 0.074 1634 Dihedral : 4.837 51.647 1293 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 2.82 % Allowed : 25.55 % Favored : 71.64 % 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: 0.50 (0.25), residues: 1160 helix: 1.81 (0.25), residues: 443 sheet: -0.07 (0.34), residues: 239 loop : -0.84 (0.29), residues: 478 ********************** 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 149 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.127 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 23 residues processed: 143 average time/residue: 1.1212 time to fit residues: 172.8850 Evaluate side-chains 144 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 4 average time/residue: 0.3744 time to fit residues: 3.1465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 0.0050 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 0.0370 chunk 5 optimal weight: 0.0020 chunk 64 optimal weight: 4.9990 overall best weight: 0.2680 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.075515 restraints weight = 19157.710| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.41 r_work: 0.2962 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3799 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= 0.203 Angle : 0.724 12.404 12743 Z= 0.355 Chirality : 0.041 0.144 1414 Planarity : 0.004 0.073 1634 Dihedral : 4.660 52.822 1293 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 2.50 % Allowed : 26.28 % Favored : 71.22 % 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: 0.61 (0.26), residues: 1160 helix: 1.88 (0.25), residues: 443 sheet: -0.08 (0.34), residues: 236 loop : -0.71 (0.29), residues: 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3805.87 seconds wall clock time: 68 minutes 14.14 seconds (4094.14 seconds total)