Starting phenix.real_space_refine on Fri Dec 27 12:25:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl9_25195/12_2024/7sl9_25195_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl9_25195/12_2024/7sl9_25195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sl9_25195/12_2024/7sl9_25195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl9_25195/12_2024/7sl9_25195.map" model { file = "/net/cci-nas-00/data/ceres_data/7sl9_25195/12_2024/7sl9_25195_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl9_25195/12_2024/7sl9_25195_neut.cif" } resolution = 3.5 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= 0.007 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 28 5.16 5 C 3091 2.51 5 N 749 2.21 5 O 844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4712 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3763 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 477} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BUA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.33, per 1000 atoms: 0.71 Number of scatterers: 4712 At special positions: 0 Unit cell: (91.16, 77.38, 90.1, 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 28 16.00 O 844 8.00 N 749 7.00 C 3091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 577.0 milliseconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 64.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 14 through 34 removed outlier: 3.795A pdb=" N SER A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.529A pdb=" N ALA A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.569A pdb=" N LEU A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.815A pdb=" N ARG A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 102 removed outlier: 3.502A pdb=" N THR A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 110 removed outlier: 3.776A pdb=" N PHE A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.721A pdb=" N LEU A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 159 removed outlier: 3.689A pdb=" N GLY A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Proline residue: A 150 - end of helix removed outlier: 4.035A pdb=" N GLN A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.880A pdb=" N VAL A 167 " --> pdb=" O TRP A 163 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 212 removed outlier: 3.991A pdb=" N PHE A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 4.029A pdb=" N ASN A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 258 removed outlier: 3.801A pdb=" N ILE A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 263 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 272 through 305 removed outlier: 3.652A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.510A pdb=" N GLN A 321 " --> pdb=" O ALA A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.622A pdb=" N LEU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 369 removed outlier: 3.564A pdb=" N PHE A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY A 348 " --> pdb=" O CYS A 344 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 350 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.730A pdb=" N GLN A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 403 removed outlier: 3.981A pdb=" N VAL A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 419 removed outlier: 3.531A pdb=" N VAL A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 433 removed outlier: 3.846A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 463 removed outlier: 3.787A pdb=" N VAL A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 525 through 533 removed outlier: 4.139A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 543 removed outlier: 3.690A pdb=" N SER A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 removed outlier: 4.051A pdb=" N LYS B 66 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9 removed outlier: 3.775A pdb=" N THR B 79 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.741A pdb=" N ALA B 93 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.592A pdb=" N TYR B 111 " --> pdb=" O TYR B 101 " (cutoff:3.500A) 228 hydrogen bonds defined for protein. 666 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: 1.16 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1428 1.34 - 1.46: 1175 1.46 - 1.58: 2183 1.58 - 1.70: 0 1.70 - 1.81: 43 Bond restraints: 4829 Sorted by residual: bond pdb=" C THR A 510 " pdb=" N PRO A 511 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.08e-02 8.57e+03 4.38e+00 bond pdb=" C SER A 317 " pdb=" N ALA A 318 " ideal model delta sigma weight residual 1.329 1.276 0.052 3.03e-02 1.09e+03 2.99e+00 bond pdb=" C3 BUA A 701 " pdb=" C4 BUA A 701 " ideal model delta sigma weight residual 1.539 1.506 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" N LYS A 314 " pdb=" CA LYS A 314 " ideal model delta sigma weight residual 1.460 1.485 -0.024 1.51e-02 4.39e+03 2.58e+00 bond pdb=" N VAL A 316 " pdb=" CA VAL A 316 " ideal model delta sigma weight residual 1.458 1.440 0.018 1.19e-02 7.06e+03 2.39e+00 ... (remaining 4824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 6398 2.36 - 4.71: 153 4.71 - 7.07: 31 7.07 - 9.42: 8 9.42 - 11.78: 2 Bond angle restraints: 6592 Sorted by residual: angle pdb=" N LYS A 315 " pdb=" CA LYS A 315 " pdb=" C LYS A 315 " ideal model delta sigma weight residual 110.35 122.13 -11.78 1.36e+00 5.41e-01 7.50e+01 angle pdb=" N VAL A 316 " pdb=" CA VAL A 316 " pdb=" C VAL A 316 " ideal model delta sigma weight residual 108.12 98.81 9.31 1.44e+00 4.82e-01 4.18e+01 angle pdb=" N GLN A 508 " pdb=" CA GLN A 508 " pdb=" C GLN A 508 " ideal model delta sigma weight residual 112.68 107.28 5.40 1.33e+00 5.65e-01 1.65e+01 angle pdb=" C PHE A 160 " pdb=" N ASP A 161 " pdb=" CA ASP A 161 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C THR A 178 " pdb=" N LEU A 179 " pdb=" CA LEU A 179 " ideal model delta sigma weight residual 124.31 130.91 -6.60 1.67e+00 3.59e-01 1.56e+01 ... (remaining 6587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 2473 17.66 - 35.32: 236 35.32 - 52.98: 36 52.98 - 70.64: 7 70.64 - 88.30: 2 Dihedral angle restraints: 2754 sinusoidal: 983 harmonic: 1771 Sorted by residual: dihedral pdb=" CA TYR B 111 " pdb=" C TYR B 111 " pdb=" N TYR B 112 " pdb=" CA TYR B 112 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU A 409 " pdb=" C LEU A 409 " pdb=" N LEU A 410 " pdb=" CA LEU A 410 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ILE A 477 " pdb=" C ILE A 477 " pdb=" N GLN A 478 " pdb=" CA GLN A 478 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 2751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 695 0.092 - 0.184: 67 0.184 - 0.276: 6 0.276 - 0.368: 0 0.368 - 0.460: 1 Chirality restraints: 769 Sorted by residual: chirality pdb=" CA LYS A 315 " pdb=" N LYS A 315 " pdb=" C LYS A 315 " pdb=" CB LYS A 315 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CA VAL A 316 " pdb=" N VAL A 316 " pdb=" C VAL A 316 " pdb=" CB VAL A 316 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL A 203 " pdb=" CA VAL A 203 " pdb=" CG1 VAL A 203 " pdb=" CG2 VAL A 203 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 766 not shown) Planarity restraints: 813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BUA A 701 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C4 BUA A 701 " 0.067 2.00e-02 2.50e+03 pdb=" O1 BUA A 701 " -0.024 2.00e-02 2.50e+03 pdb=" O2 BUA A 701 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 309 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A 310 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 422 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 423 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " 0.032 5.00e-02 4.00e+02 ... (remaining 810 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1296 2.79 - 3.32: 4351 3.32 - 3.84: 7690 3.84 - 4.37: 9146 4.37 - 4.90: 15370 Nonbonded interactions: 37853 Sorted by model distance: nonbonded pdb=" O PRO A 472 " pdb=" OH TYR B 111 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR B 92 " pdb=" O VAL B 120 " model vdw 2.290 3.040 nonbonded pdb=" O GLY A 224 " pdb=" OG SER B 31 " model vdw 2.304 3.040 nonbonded pdb=" O ILE A 246 " pdb=" OG1 THR A 250 " model vdw 2.304 3.040 nonbonded pdb=" O THR A 250 " pdb=" OG1 THR A 254 " model vdw 2.312 3.040 ... (remaining 37848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 0.060 4829 Z= 0.308 Angle : 0.951 11.781 6592 Z= 0.523 Chirality : 0.058 0.460 769 Planarity : 0.007 0.061 813 Dihedral : 13.950 88.296 1628 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.40 % Allowed : 9.51 % Favored : 90.08 % 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: -6.01 (0.22), residues: 611 helix: -4.33 (0.11), residues: 357 sheet: -2.43 (0.71), residues: 45 loop : -3.26 (0.35), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 516 HIS 0.004 0.002 HIS A 306 PHE 0.019 0.002 PHE A 160 TYR 0.015 0.002 TYR A 372 ARG 0.002 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 PHE cc_start: 0.9162 (t80) cc_final: 0.8863 (t80) REVERT: A 277 LYS cc_start: 0.8937 (mttt) cc_final: 0.8591 (mttp) REVERT: A 383 TRP cc_start: 0.7797 (t60) cc_final: 0.7559 (t60) REVERT: A 425 MET cc_start: 0.9033 (tmm) cc_final: 0.8483 (ttt) REVERT: A 480 CYS cc_start: 0.5398 (t) cc_final: 0.5137 (t) REVERT: A 514 ASP cc_start: 0.8187 (t0) cc_final: 0.7854 (m-30) REVERT: A 515 ASN cc_start: 0.8798 (m-40) cc_final: 0.8590 (m-40) REVERT: B 6 LEU cc_start: 0.8717 (pt) cc_final: 0.8466 (pp) REVERT: B 21 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8850 (ttp80) REVERT: B 39 TYR cc_start: 0.8364 (m-80) cc_final: 0.8008 (m-80) outliers start: 2 outliers final: 1 residues processed: 163 average time/residue: 0.1491 time to fit residues: 31.6327 Evaluate side-chains 128 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 156 GLN A 474 HIS B 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4829 Z= 0.188 Angle : 0.697 11.585 6592 Z= 0.356 Chirality : 0.043 0.190 769 Planarity : 0.005 0.042 813 Dihedral : 5.606 26.571 672 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.24 % Allowed : 18.62 % Favored : 78.14 % 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: -4.08 (0.27), residues: 611 helix: -2.44 (0.20), residues: 364 sheet: -3.15 (0.65), residues: 47 loop : -2.71 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 516 HIS 0.002 0.001 HIS A 474 PHE 0.011 0.001 PHE B 69 TYR 0.014 0.001 TYR A 108 ARG 0.005 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.7898 (mmt) cc_final: 0.7636 (mmm) REVERT: A 66 MET cc_start: 0.8160 (tpp) cc_final: 0.7890 (tpp) REVERT: A 125 LYS cc_start: 0.8886 (tptp) cc_final: 0.8487 (tptp) REVERT: A 383 TRP cc_start: 0.7681 (t60) cc_final: 0.7380 (t60) REVERT: B 6 LEU cc_start: 0.8739 (pt) cc_final: 0.8518 (pp) REVERT: B 21 ARG cc_start: 0.9138 (ttp80) cc_final: 0.8683 (ttm-80) REVERT: B 54 ASN cc_start: 0.8957 (p0) cc_final: 0.8344 (p0) REVERT: B 61 TYR cc_start: 0.8897 (m-80) cc_final: 0.8541 (m-80) REVERT: B 68 ARG cc_start: 0.7540 (ptm160) cc_final: 0.6916 (ptm160) REVERT: B 69 PHE cc_start: 0.8316 (m-10) cc_final: 0.8038 (m-80) REVERT: B 82 LEU cc_start: 0.9472 (tt) cc_final: 0.9057 (tt) REVERT: B 84 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7398 (mmp) REVERT: B 91 ASP cc_start: 0.7335 (p0) cc_final: 0.7056 (p0) outliers start: 16 outliers final: 10 residues processed: 150 average time/residue: 0.1402 time to fit residues: 27.4369 Evaluate side-chains 133 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 TYR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 0.0010 chunk 54 optimal weight: 4.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4829 Z= 0.187 Angle : 0.674 11.041 6592 Z= 0.335 Chirality : 0.042 0.151 769 Planarity : 0.004 0.035 813 Dihedral : 5.157 24.368 672 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.05 % Allowed : 20.85 % Favored : 75.10 % 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: -3.01 (0.31), residues: 611 helix: -1.45 (0.24), residues: 372 sheet: -3.31 (0.61), residues: 47 loop : -2.41 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 516 HIS 0.002 0.001 HIS A 240 PHE 0.011 0.001 PHE A 436 TYR 0.015 0.001 TYR A 176 ARG 0.005 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.8813 (t80) cc_final: 0.8549 (t80) REVERT: A 52 MET cc_start: 0.7256 (mmm) cc_final: 0.6886 (mmm) REVERT: A 219 ASN cc_start: 0.8455 (t0) cc_final: 0.8029 (t0) REVERT: A 383 TRP cc_start: 0.7648 (t60) cc_final: 0.7339 (t60) REVERT: B 21 ARG cc_start: 0.9149 (ttp80) cc_final: 0.8700 (ttm-80) REVERT: B 48 GLU cc_start: 0.8300 (tt0) cc_final: 0.7942 (tt0) REVERT: B 53 ILE cc_start: 0.8094 (pt) cc_final: 0.7799 (pt) REVERT: B 54 ASN cc_start: 0.8942 (p0) cc_final: 0.8209 (p0) REVERT: B 61 TYR cc_start: 0.8899 (m-80) cc_final: 0.8528 (m-80) REVERT: B 82 LEU cc_start: 0.9390 (tt) cc_final: 0.8737 (tp) REVERT: B 109 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7114 (p0) outliers start: 20 outliers final: 12 residues processed: 145 average time/residue: 0.1628 time to fit residues: 30.7060 Evaluate side-chains 137 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 49 optimal weight: 0.8980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4829 Z= 0.208 Angle : 0.696 10.853 6592 Z= 0.342 Chirality : 0.043 0.126 769 Planarity : 0.004 0.035 813 Dihedral : 5.115 24.446 672 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.26 % Allowed : 20.45 % Favored : 74.29 % 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: -2.34 (0.32), residues: 611 helix: -0.84 (0.26), residues: 372 sheet: -3.06 (0.66), residues: 49 loop : -2.31 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.002 0.001 HIS A 240 PHE 0.024 0.001 PHE A 65 TYR 0.011 0.001 TYR A 32 ARG 0.005 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 31 TYR cc_start: 0.8790 (t80) cc_final: 0.8565 (t80) REVERT: A 219 ASN cc_start: 0.8432 (t0) cc_final: 0.8009 (t0) REVERT: A 383 TRP cc_start: 0.7695 (t60) cc_final: 0.7419 (t60) REVERT: A 436 PHE cc_start: 0.7890 (p90) cc_final: 0.7528 (p90) REVERT: B 21 ARG cc_start: 0.9168 (ttp80) cc_final: 0.8725 (tpp80) REVERT: B 54 ASN cc_start: 0.8920 (p0) cc_final: 0.8251 (p0) REVERT: B 82 LEU cc_start: 0.9358 (tt) cc_final: 0.8922 (tt) REVERT: B 109 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7118 (p0) outliers start: 26 outliers final: 24 residues processed: 151 average time/residue: 0.1457 time to fit residues: 28.7538 Evaluate side-chains 154 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4829 Z= 0.215 Angle : 0.717 11.101 6592 Z= 0.352 Chirality : 0.043 0.128 769 Planarity : 0.004 0.036 813 Dihedral : 5.161 24.838 672 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 7.09 % Allowed : 19.64 % Favored : 73.28 % 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: -1.97 (0.33), residues: 611 helix: -0.52 (0.26), residues: 371 sheet: -2.99 (0.70), residues: 49 loop : -2.18 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 187 HIS 0.002 0.001 HIS A 240 PHE 0.025 0.001 PHE A 160 TYR 0.024 0.001 TYR B 61 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8956 (tptp) cc_final: 0.8472 (tptp) REVERT: A 219 ASN cc_start: 0.8421 (t0) cc_final: 0.8012 (t0) REVERT: A 290 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8886 (tt) REVERT: A 383 TRP cc_start: 0.7709 (t60) cc_final: 0.7420 (t60) REVERT: A 436 PHE cc_start: 0.7905 (p90) cc_final: 0.7575 (p90) REVERT: B 21 ARG cc_start: 0.9173 (ttp80) cc_final: 0.8779 (tpp80) REVERT: B 41 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8348 (tm-30) REVERT: B 54 ASN cc_start: 0.8923 (p0) cc_final: 0.8183 (p0) REVERT: B 68 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7448 (ptm160) REVERT: B 69 PHE cc_start: 0.8777 (m-80) cc_final: 0.8040 (m-80) REVERT: B 82 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8884 (tt) REVERT: B 91 ASP cc_start: 0.7094 (p0) cc_final: 0.6574 (p0) REVERT: B 109 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7092 (p0) outliers start: 35 outliers final: 26 residues processed: 157 average time/residue: 0.1624 time to fit residues: 33.3972 Evaluate side-chains 155 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 461 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4829 Z= 0.202 Angle : 0.716 10.237 6592 Z= 0.351 Chirality : 0.043 0.129 769 Planarity : 0.004 0.034 813 Dihedral : 5.151 24.328 672 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.87 % Allowed : 22.47 % Favored : 71.66 % 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: -1.76 (0.34), residues: 611 helix: -0.33 (0.27), residues: 370 sheet: -2.87 (0.71), residues: 47 loop : -2.19 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 253 HIS 0.002 0.001 HIS A 306 PHE 0.019 0.001 PHE A 65 TYR 0.012 0.001 TYR A 32 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8938 (tptp) cc_final: 0.8445 (tptp) REVERT: A 219 ASN cc_start: 0.8461 (t0) cc_final: 0.8020 (t0) REVERT: A 290 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 383 TRP cc_start: 0.7700 (t60) cc_final: 0.7420 (t60) REVERT: A 436 PHE cc_start: 0.7920 (p90) cc_final: 0.7601 (p90) REVERT: B 21 ARG cc_start: 0.9156 (ttp80) cc_final: 0.8860 (tpp80) REVERT: B 54 ASN cc_start: 0.8892 (p0) cc_final: 0.8184 (p0) REVERT: B 69 PHE cc_start: 0.8790 (m-80) cc_final: 0.8556 (m-80) REVERT: B 82 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8782 (tp) REVERT: B 91 ASP cc_start: 0.7109 (p0) cc_final: 0.6691 (p0) REVERT: B 109 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.6986 (p0) outliers start: 29 outliers final: 23 residues processed: 150 average time/residue: 0.1452 time to fit residues: 28.5627 Evaluate side-chains 155 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN B 5 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4829 Z= 0.244 Angle : 0.723 9.137 6592 Z= 0.357 Chirality : 0.044 0.135 769 Planarity : 0.004 0.031 813 Dihedral : 5.185 29.730 672 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.87 % Allowed : 22.87 % Favored : 71.26 % 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: -1.65 (0.34), residues: 611 helix: -0.24 (0.27), residues: 370 sheet: -2.83 (0.69), residues: 47 loop : -2.12 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 311 HIS 0.002 0.001 HIS A 240 PHE 0.032 0.001 PHE A 65 TYR 0.016 0.001 TYR A 32 ARG 0.005 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.668 Fit side-chains REVERT: A 125 LYS cc_start: 0.8914 (tptp) cc_final: 0.8554 (tptp) REVERT: A 219 ASN cc_start: 0.8473 (t0) cc_final: 0.8033 (t0) REVERT: A 383 TRP cc_start: 0.7724 (t60) cc_final: 0.7433 (t60) REVERT: A 436 PHE cc_start: 0.7950 (p90) cc_final: 0.7646 (p90) REVERT: B 21 ARG cc_start: 0.9127 (ttp80) cc_final: 0.8842 (tpp80) REVERT: B 53 ILE cc_start: 0.7719 (pt) cc_final: 0.7384 (pt) REVERT: B 54 ASN cc_start: 0.8995 (p0) cc_final: 0.8257 (p0) REVERT: B 82 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8793 (tp) REVERT: B 91 ASP cc_start: 0.6836 (p0) cc_final: 0.6543 (p0) REVERT: B 109 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7068 (p0) outliers start: 29 outliers final: 24 residues processed: 146 average time/residue: 0.1523 time to fit residues: 29.0536 Evaluate side-chains 147 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.0050 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN B 5 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4829 Z= 0.190 Angle : 0.713 9.392 6592 Z= 0.352 Chirality : 0.043 0.136 769 Planarity : 0.004 0.033 813 Dihedral : 5.021 27.452 672 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.86 % Allowed : 24.70 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.34), residues: 611 helix: -0.16 (0.27), residues: 372 sheet: -2.83 (0.67), residues: 49 loop : -2.13 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.002 0.001 HIS A 306 PHE 0.028 0.001 PHE A 65 TYR 0.017 0.001 TYR A 176 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8361 (t0) cc_final: 0.7983 (t0) REVERT: A 383 TRP cc_start: 0.7684 (t60) cc_final: 0.7407 (t60) REVERT: A 436 PHE cc_start: 0.7900 (p90) cc_final: 0.7608 (p90) REVERT: B 21 ARG cc_start: 0.9015 (ttp80) cc_final: 0.8774 (tpp80) REVERT: B 54 ASN cc_start: 0.8931 (p0) cc_final: 0.8258 (p0) REVERT: B 82 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8769 (tp) REVERT: B 109 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6925 (p0) outliers start: 24 outliers final: 20 residues processed: 153 average time/residue: 0.1765 time to fit residues: 34.0901 Evaluate side-chains 153 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 35 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4829 Z= 0.181 Angle : 0.720 9.030 6592 Z= 0.357 Chirality : 0.043 0.154 769 Planarity : 0.004 0.036 813 Dihedral : 4.981 26.701 672 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.45 % Allowed : 25.91 % Favored : 69.64 % 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: -1.49 (0.34), residues: 611 helix: -0.08 (0.27), residues: 372 sheet: -2.63 (0.63), residues: 52 loop : -2.17 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 55 HIS 0.003 0.001 HIS A 306 PHE 0.036 0.001 PHE A 160 TYR 0.018 0.001 TYR A 32 ARG 0.008 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.485 Fit side-chains REVERT: A 219 ASN cc_start: 0.8320 (t0) cc_final: 0.7900 (t0) REVERT: A 277 LYS cc_start: 0.8955 (mttt) cc_final: 0.8679 (mttt) REVERT: A 281 TYR cc_start: 0.8703 (m-80) cc_final: 0.8479 (m-80) REVERT: A 341 PHE cc_start: 0.8088 (t80) cc_final: 0.7868 (t80) REVERT: A 383 TRP cc_start: 0.7614 (t60) cc_final: 0.7355 (t60) REVERT: A 436 PHE cc_start: 0.7934 (p90) cc_final: 0.7652 (p90) REVERT: B 20 LEU cc_start: 0.8619 (tt) cc_final: 0.8239 (mm) REVERT: B 21 ARG cc_start: 0.8998 (ttp80) cc_final: 0.8717 (tpp80) REVERT: B 54 ASN cc_start: 0.8965 (p0) cc_final: 0.8290 (p0) REVERT: B 68 ARG cc_start: 0.7639 (ttp-110) cc_final: 0.7227 (ttt-90) REVERT: B 82 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8848 (tp) REVERT: B 84 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7295 (mmp) REVERT: B 109 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6918 (p0) outliers start: 22 outliers final: 17 residues processed: 143 average time/residue: 0.1593 time to fit residues: 29.6581 Evaluate side-chains 148 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 38 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4829 Z= 0.202 Angle : 0.748 9.121 6592 Z= 0.369 Chirality : 0.044 0.153 769 Planarity : 0.004 0.040 813 Dihedral : 4.982 26.301 672 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.85 % Allowed : 26.92 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.34), residues: 611 helix: -0.06 (0.27), residues: 374 sheet: -2.89 (0.59), residues: 52 loop : -2.18 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 55 HIS 0.002 0.001 HIS A 306 PHE 0.033 0.001 PHE A 160 TYR 0.020 0.001 TYR A 176 ARG 0.006 0.001 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8425 (t0) cc_final: 0.7927 (t0) REVERT: A 277 LYS cc_start: 0.8953 (mttt) cc_final: 0.8628 (mttp) REVERT: A 281 TYR cc_start: 0.8650 (m-80) cc_final: 0.8402 (m-80) REVERT: A 436 PHE cc_start: 0.7951 (p90) cc_final: 0.7670 (p90) REVERT: B 20 LEU cc_start: 0.8628 (tt) cc_final: 0.8242 (mm) REVERT: B 54 ASN cc_start: 0.8969 (p0) cc_final: 0.8270 (p0) REVERT: B 68 ARG cc_start: 0.7651 (ttp-110) cc_final: 0.7298 (ttt-90) REVERT: B 84 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7228 (mmp) REVERT: B 109 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7017 (p0) outliers start: 19 outliers final: 16 residues processed: 135 average time/residue: 0.1506 time to fit residues: 26.7196 Evaluate side-chains 138 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110749 restraints weight = 7624.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114407 restraints weight = 4126.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116782 restraints weight = 2904.020| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4829 Z= 0.255 Angle : 0.768 8.781 6592 Z= 0.379 Chirality : 0.045 0.139 769 Planarity : 0.004 0.042 813 Dihedral : 5.100 26.132 672 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.45 % Allowed : 26.11 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.34), residues: 611 helix: -0.06 (0.27), residues: 370 sheet: -2.75 (0.60), residues: 51 loop : -2.10 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.002 0.001 HIS A 240 PHE 0.036 0.002 PHE A 160 TYR 0.013 0.001 TYR A 463 ARG 0.006 0.001 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1347.48 seconds wall clock time: 25 minutes 4.33 seconds (1504.33 seconds total)