Starting phenix.real_space_refine on Fri Oct 11 00:08:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/10_2024/7rtb_24680.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/10_2024/7rtb_24680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/10_2024/7rtb_24680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/10_2024/7rtb_24680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/10_2024/7rtb_24680.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/10_2024/7rtb_24680.cif" } resolution = 2.14 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 5693 2.51 5 N 1568 2.21 5 O 1660 1.98 5 H 7 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1949 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2796 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 553 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 8, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 277 Chain: "P" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.77, per 1000 atoms: 0.64 Number of scatterers: 8979 At special positions: 0 Unit cell: (81.9, 96.85, 170.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 1660 8.00 N 1568 7.00 C 5693 6.00 H 7 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, 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=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 44.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.883A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.516A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.563A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 4.415A pdb=" N TYR A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.610A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.688A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.657A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.970A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.605A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.854A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.748A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 53 removed outlier: 3.640A pdb=" N GLN R 37 " --> pdb=" O TRP R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 4.172A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 169 removed outlier: 3.612A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 199 Processing helix chain 'R' and resid 199 through 211 removed outlier: 3.859A pdb=" N THR R 207 " --> pdb=" O TRP R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 223 Processing helix chain 'R' and resid 225 through 257 removed outlier: 3.581A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.695A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 3.782A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.650A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR R 291 " --> pdb=" O VAL R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 298 removed outlier: 4.088A pdb=" N CYS R 296 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 308 removed outlier: 3.603A pdb=" N LEU R 307 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE R 308 " --> pdb=" O TYR R 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 304 through 308' Processing helix chain 'R' and resid 309 through 338 removed outlier: 3.823A pdb=" N ASN R 320 " --> pdb=" O ALA R 316 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE R 324 " --> pdb=" O ASN R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 361 removed outlier: 3.703A pdb=" N LEU R 354 " --> pdb=" O ALA R 350 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 371 Processing helix chain 'R' and resid 382 through 403 removed outlier: 5.104A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 removed outlier: 4.056A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 26 Processing helix chain 'P' and resid 27 through 29 No H-bonds generated for 'chain 'P' and resid 27 through 29' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.396A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.769A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.968A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.083A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.582A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.673A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.571A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.672A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.679A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 removed outlier: 3.527A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP R 72 " --> pdb=" O THR R 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 80 through 84 472 hydrogen bonds defined for protein. 1350 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: 2.65 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 7 1.09 - 1.27: 1478 1.27 - 1.45: 2572 1.45 - 1.63: 5026 1.63 - 1.81: 71 Bond restraints: 9154 Sorted by residual: bond pdb=" C ALA B 106 " pdb=" N PRO B 107 " ideal model delta sigma weight residual 1.333 1.379 -0.046 1.44e-02 4.82e+03 1.01e+01 bond pdb=" N ILE P 12 " pdb=" CA ILE P 12 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.82e+00 bond pdb=" N VAL P 23 " pdb=" CA VAL P 23 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.66e+00 bond pdb=" N ASN R 320 " pdb=" CA ASN R 320 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.36e+00 bond pdb=" N LEU P 26 " pdb=" CA LEU P 26 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.30e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 11767 1.15 - 2.30: 497 2.30 - 3.46: 130 3.46 - 4.61: 19 4.61 - 5.76: 7 Bond angle restraints: 12420 Sorted by residual: angle pdb=" C ALA B 106 " pdb=" N PRO B 107 " pdb=" CA PRO B 107 " ideal model delta sigma weight residual 119.47 125.13 -5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 122.75 -2.51 6.30e-01 2.52e+00 1.59e+01 angle pdb=" N ASN P 24 " pdb=" CA ASN P 24 " pdb=" C ASN P 24 " ideal model delta sigma weight residual 111.28 107.62 3.66 1.09e+00 8.42e-01 1.13e+01 angle pdb=" N TRP R 417 " pdb=" CA TRP R 417 " pdb=" C TRP R 417 " ideal model delta sigma weight residual 113.55 109.58 3.97 1.26e+00 6.30e-01 9.92e+00 angle pdb=" C VAL R 276 " pdb=" CA VAL R 276 " pdb=" CB VAL R 276 " ideal model delta sigma weight residual 114.35 111.21 3.14 1.06e+00 8.90e-01 8.80e+00 ... (remaining 12415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4922 17.92 - 35.85: 389 35.85 - 53.77: 79 53.77 - 71.70: 17 71.70 - 89.62: 13 Dihedral angle restraints: 5420 sinusoidal: 2019 harmonic: 3401 Sorted by residual: dihedral pdb=" CA ASN R 320 " pdb=" C ASN R 320 " pdb=" N PHE R 321 " pdb=" CA PHE R 321 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 1.99e+01 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 -120.51 34.51 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1084 0.045 - 0.090: 231 0.090 - 0.135: 73 0.135 - 0.180: 11 0.180 - 0.226: 2 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CA LYS P 16 " pdb=" N LYS P 16 " pdb=" C LYS P 16 " pdb=" CB LYS P 16 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA LEU P 14 " pdb=" N LEU P 14 " pdb=" C LEU P 14 " pdb=" CB LEU P 14 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1398 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 19 " -0.012 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" N AIB P 20 " 0.037 2.00e-02 2.50e+03 pdb=" CA AIB P 20 " -0.010 2.00e-02 2.50e+03 pdb=" H AIB P 20 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO N 88 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 315 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.33e+00 pdb=" C PHE R 315 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE R 315 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA R 316 " -0.009 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.64: 88 2.64 - 3.13: 6623 3.13 - 3.62: 11012 3.62 - 4.11: 15348 4.11 - 4.60: 22943 Nonbonded interactions: 56014 Sorted by model distance: nonbonded pdb=" H AIB P 20 " pdb="HB22 AIB P 20 " model vdw 2.151 2.270 nonbonded pdb=" O LEU R 172 " pdb=" ND2 ASN R 177 " model vdw 2.277 2.950 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.311 2.800 nonbonded pdb="HB12 AIB P 20 " pdb="HB23 AIB P 20 " model vdw 2.328 2.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OE1 GLU A 230 " model vdw 2.335 2.950 ... (remaining 56009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.260 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: 0.270 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 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 : 0.003 0.046 9147 Z= 0.189 Angle : 0.568 5.760 12406 Z= 0.386 Chirality : 0.043 0.226 1401 Planarity : 0.003 0.046 1588 Dihedral : 14.485 89.621 3208 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.77 % Allowed : 8.96 % Favored : 90.27 % 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: -0.80 (0.23), residues: 1144 helix: 0.35 (0.23), residues: 459 sheet: -0.46 (0.32), residues: 232 loop : -1.40 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 PHE 0.009 0.001 PHE A 212 TYR 0.011 0.001 TYR P 13 ARG 0.002 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.7105 (m-30) cc_final: 0.6851 (m-30) outliers start: 7 outliers final: 3 residues processed: 164 average time/residue: 1.3889 time to fit residues: 241.9336 Evaluate side-chains 114 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.0040 chunk 103 optimal weight: 5.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 213 GLN A 218 ASN A 254 ASN A 292 ASN B 36 ASN B 44 GLN B 175 GLN B 259 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9147 Z= 0.115 Angle : 0.396 3.978 12406 Z= 0.221 Chirality : 0.037 0.126 1401 Planarity : 0.003 0.034 1588 Dihedral : 3.668 32.040 1273 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.99 % Allowed : 14.93 % Favored : 82.08 % 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: 1.07 (0.25), residues: 1144 helix: 2.26 (0.25), residues: 457 sheet: 0.04 (0.32), residues: 243 loop : -0.53 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.012 0.001 TYR P 13 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5172 (mmt180) REVERT: B 186 ASP cc_start: 0.7735 (m-30) cc_final: 0.7476 (m-30) REVERT: N 34 MET cc_start: 0.6786 (mmm) cc_final: 0.6396 (mmm) REVERT: R 362 THR cc_start: 0.7359 (OUTLIER) cc_final: 0.7010 (p) outliers start: 27 outliers final: 9 residues processed: 131 average time/residue: 1.4621 time to fit residues: 202.8388 Evaluate side-chains 121 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 213 GLN A 267 GLN B 44 GLN B 110 ASN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 35 ASN N 39 GLN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9147 Z= 0.367 Angle : 0.619 8.337 12406 Z= 0.340 Chirality : 0.045 0.158 1401 Planarity : 0.005 0.042 1588 Dihedral : 4.803 46.867 1270 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.87 % Allowed : 16.81 % Favored : 79.31 % 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: 0.94 (0.25), residues: 1144 helix: 2.10 (0.24), residues: 452 sheet: -0.00 (0.32), residues: 236 loop : -0.51 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 234 HIS 0.013 0.002 HIS A 357 PHE 0.018 0.002 PHE R 280 TYR 0.016 0.003 TYR R 235 ARG 0.007 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 1.234 Fit side-chains REVERT: B 42 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.5547 (mmt180) outliers start: 35 outliers final: 18 residues processed: 144 average time/residue: 1.3813 time to fit residues: 211.0771 Evaluate side-chains 134 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 390 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 213 GLN B 44 GLN B 175 GLN B 176 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9147 Z= 0.181 Angle : 0.457 4.991 12406 Z= 0.255 Chirality : 0.039 0.134 1401 Planarity : 0.003 0.036 1588 Dihedral : 4.377 48.839 1270 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.87 % Allowed : 18.25 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1144 helix: 2.55 (0.24), residues: 458 sheet: 0.31 (0.33), residues: 216 loop : -0.56 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.014 0.002 TYR R 305 ARG 0.003 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6398 (OUTLIER) cc_final: 0.5378 (mmt180) REVERT: B 59 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7472 (t80) REVERT: B 155 ASN cc_start: 0.6349 (OUTLIER) cc_final: 0.6063 (t0) REVERT: N 6 GLU cc_start: 0.5712 (mp0) cc_final: 0.5501 (mp0) outliers start: 35 outliers final: 17 residues processed: 142 average time/residue: 1.3458 time to fit residues: 203.3628 Evaluate side-chains 140 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 390 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 40.0000 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 0.0370 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 213 GLN B 44 GLN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9147 Z= 0.305 Angle : 0.561 7.533 12406 Z= 0.309 Chirality : 0.043 0.150 1401 Planarity : 0.004 0.042 1588 Dihedral : 4.820 52.872 1270 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.98 % Allowed : 18.03 % Favored : 76.99 % 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: 0.99 (0.25), residues: 1144 helix: 2.31 (0.24), residues: 457 sheet: 0.01 (0.32), residues: 230 loop : -0.70 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.010 0.002 HIS A 357 PHE 0.019 0.002 PHE B 151 TYR 0.016 0.002 TYR R 242 ARG 0.005 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 122 time to evaluate : 1.053 Fit side-chains REVERT: B 42 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5459 (mmp-170) REVERT: B 155 ASN cc_start: 0.6506 (OUTLIER) cc_final: 0.6150 (t0) REVERT: N 19 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6055 (ttm170) outliers start: 45 outliers final: 28 residues processed: 146 average time/residue: 1.3217 time to fit residues: 205.3332 Evaluate side-chains 149 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 390 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 213 GLN A 357 HIS B 44 GLN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9147 Z= 0.131 Angle : 0.421 4.397 12406 Z= 0.236 Chirality : 0.038 0.133 1401 Planarity : 0.003 0.039 1588 Dihedral : 4.307 53.446 1270 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.98 % Allowed : 19.14 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1144 helix: 2.82 (0.24), residues: 464 sheet: 0.39 (0.34), residues: 216 loop : -0.64 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.014 0.001 TYR R 305 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.118 Fit side-chains REVERT: B 42 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.5404 (mmt180) REVERT: B 59 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 155 ASN cc_start: 0.6406 (OUTLIER) cc_final: 0.6091 (t0) REVERT: R 294 GLU cc_start: 0.4941 (OUTLIER) cc_final: 0.4488 (tp30) REVERT: P 21 GLU cc_start: 0.1929 (OUTLIER) cc_final: 0.1689 (pp20) outliers start: 36 outliers final: 18 residues processed: 140 average time/residue: 1.3997 time to fit residues: 208.6123 Evaluate side-chains 137 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain P residue 21 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 0.0050 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.0170 chunk 67 optimal weight: 5.9990 overall best weight: 1.5434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS B 44 GLN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9147 Z= 0.170 Angle : 0.453 4.695 12406 Z= 0.251 Chirality : 0.039 0.136 1401 Planarity : 0.003 0.039 1588 Dihedral : 4.348 53.565 1270 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.20 % Allowed : 19.03 % Favored : 76.77 % 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: 1.62 (0.25), residues: 1144 helix: 2.96 (0.24), residues: 464 sheet: 0.38 (0.34), residues: 217 loop : -0.58 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.012 0.001 TYR R 242 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.085 Fit side-chains REVERT: B 42 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5457 (mmt180) REVERT: B 59 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7491 (t80) REVERT: B 155 ASN cc_start: 0.6436 (OUTLIER) cc_final: 0.6112 (t0) REVERT: R 294 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.4571 (tp30) outliers start: 38 outliers final: 25 residues processed: 139 average time/residue: 1.3532 time to fit residues: 199.9722 Evaluate side-chains 143 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 0.2980 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 35 GLN A 54 ASN A 357 HIS B 44 GLN B 175 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9147 Z= 0.128 Angle : 0.422 4.476 12406 Z= 0.234 Chirality : 0.038 0.131 1401 Planarity : 0.003 0.039 1588 Dihedral : 4.191 53.429 1270 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.76 % Allowed : 19.69 % Favored : 76.55 % 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: 1.80 (0.26), residues: 1144 helix: 3.18 (0.24), residues: 464 sheet: 0.50 (0.34), residues: 216 loop : -0.57 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR R 242 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 1.094 Fit side-chains REVERT: B 42 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.5408 (mmt180) REVERT: B 59 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7535 (t80) REVERT: B 155 ASN cc_start: 0.6404 (OUTLIER) cc_final: 0.6088 (t0) REVERT: R 294 GLU cc_start: 0.5001 (OUTLIER) cc_final: 0.4584 (tp30) REVERT: P 21 GLU cc_start: 0.1841 (OUTLIER) cc_final: 0.1611 (pp20) outliers start: 34 outliers final: 22 residues processed: 137 average time/residue: 1.3780 time to fit residues: 200.6723 Evaluate side-chains 140 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain P residue 21 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 40.0000 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9147 Z= 0.344 Angle : 0.587 8.219 12406 Z= 0.322 Chirality : 0.044 0.161 1401 Planarity : 0.005 0.045 1588 Dihedral : 4.847 54.942 1270 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.09 % Allowed : 19.47 % Favored : 76.44 % 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: 1.23 (0.25), residues: 1144 helix: 2.60 (0.24), residues: 458 sheet: 0.08 (0.33), residues: 230 loop : -0.66 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.009 0.002 HIS A 357 PHE 0.020 0.002 PHE B 151 TYR 0.018 0.002 TYR R 242 ARG 0.007 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 0.837 Fit side-chains REVERT: B 42 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.5611 (mmp-170) REVERT: B 155 ASN cc_start: 0.6502 (OUTLIER) cc_final: 0.6152 (t0) REVERT: N 19 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6078 (ttm170) REVERT: R 294 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.4669 (tp30) REVERT: R 390 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.6075 (t80) REVERT: P 21 GLU cc_start: 0.1906 (OUTLIER) cc_final: 0.1602 (pp20) outliers start: 37 outliers final: 24 residues processed: 140 average time/residue: 1.3521 time to fit residues: 201.6165 Evaluate side-chains 142 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain P residue 21 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN B 44 GLN B 175 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9147 Z= 0.146 Angle : 0.448 6.065 12406 Z= 0.248 Chirality : 0.039 0.133 1401 Planarity : 0.003 0.040 1588 Dihedral : 4.386 55.981 1270 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.43 % Allowed : 20.35 % Favored : 76.22 % 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: 1.61 (0.25), residues: 1144 helix: 3.03 (0.24), residues: 464 sheet: 0.36 (0.34), residues: 217 loop : -0.67 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.010 0.001 TYR A 339 ARG 0.006 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.092 Fit side-chains REVERT: B 42 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.5560 (mmt180) REVERT: B 59 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7530 (t80) REVERT: B 155 ASN cc_start: 0.6426 (OUTLIER) cc_final: 0.6102 (t0) REVERT: R 294 GLU cc_start: 0.5064 (OUTLIER) cc_final: 0.4656 (tp30) REVERT: P 21 GLU cc_start: 0.1780 (OUTLIER) cc_final: 0.1550 (pp20) outliers start: 31 outliers final: 23 residues processed: 132 average time/residue: 1.4134 time to fit residues: 198.1331 Evaluate side-chains 141 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain P residue 21 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN B 175 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.186711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130045 restraints weight = 10566.467| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.87 r_work: 0.3571 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9147 Z= 0.262 Angle : 0.531 6.375 12406 Z= 0.291 Chirality : 0.042 0.145 1401 Planarity : 0.004 0.039 1588 Dihedral : 4.669 56.524 1270 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.54 % Allowed : 20.46 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1144 helix: 2.86 (0.24), residues: 458 sheet: 0.11 (0.33), residues: 229 loop : -0.65 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.010 0.002 HIS A 357 PHE 0.019 0.002 PHE B 151 TYR 0.015 0.002 TYR R 242 ARG 0.007 0.001 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4806.38 seconds wall clock time: 86 minutes 24.02 seconds (5184.02 seconds total)