Starting phenix.real_space_refine on Wed Feb 12 18:09:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsk_30835/02_2025/7dsk_30835_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsk_30835/02_2025/7dsk_30835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsk_30835/02_2025/7dsk_30835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsk_30835/02_2025/7dsk_30835.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsk_30835/02_2025/7dsk_30835_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsk_30835/02_2025/7dsk_30835_neut.cif" } resolution = 2.9 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= 0.003 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 P 1 5.49 5 S 27 5.16 5 C 4936 2.51 5 N 1191 2.21 5 O 1369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7524 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3670 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 108 Unusual residues: {'HNX': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 12} Link IDs: {None: 14} Time building chain proxies: 5.35, per 1000 atoms: 0.71 Number of scatterers: 7524 At special positions: 0 Unit cell: (83.699, 82.612, 125.005, 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 27 16.00 P 1 15.00 O 1369 8.00 N 1191 7.00 C 4936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 936.6 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 57.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 178 through 206 Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.590A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.893A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.546A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.848A pdb=" N VAL A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 357 through 372 removed outlier: 3.860A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.871A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.565A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.557A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.604A pdb=" N LEU A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 71 through 80 Processing helix chain 'B' and resid 81 through 110 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.701A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 139 through 157 removed outlier: 3.671A pdb=" N SER B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 189 Processing helix chain 'B' and resid 189 through 220 removed outlier: 3.715A pdb=" N ALA B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 4.074A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 274 through 298 Proline residue: B 283 - end of helix removed outlier: 3.503A pdb=" N THR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 3.716A pdb=" N GLY B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 422 removed outlier: 3.505A pdb=" N PHE B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 451 Processing helix chain 'B' and resid 454 through 466 removed outlier: 4.269A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 removed outlier: 4.171A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 501 removed outlier: 4.045A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.482A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 3.676A pdb=" N LYS A 267 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.766A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA5, first strand: chain 'B' and resid 365 through 366 376 hydrogen bonds defined for protein. 1083 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: 2.27 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1170 1.31 - 1.43: 2057 1.43 - 1.56: 4410 1.56 - 1.68: 23 1.68 - 1.81: 41 Bond restraints: 7701 Sorted by residual: bond pdb=" CAI Y01 B 603 " pdb=" CAZ Y01 B 603 " ideal model delta sigma weight residual 1.332 1.557 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CAI Y01 B 602 " pdb=" CAZ Y01 B 602 " ideal model delta sigma weight residual 1.332 1.548 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C02 HNX B 601 " pdb=" C07 HNX B 601 " ideal model delta sigma weight residual 1.507 1.707 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C09 HNX B 601 " pdb=" C10 HNX B 601 " ideal model delta sigma weight residual 1.523 1.323 0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" C18 HNX B 601 " pdb=" C19 HNX B 601 " ideal model delta sigma weight residual 1.411 1.564 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 7696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 10211 2.95 - 5.91: 216 5.91 - 8.86: 49 8.86 - 11.82: 8 11.82 - 14.77: 4 Bond angle restraints: 10488 Sorted by residual: angle pdb=" C PRO A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta sigma weight residual 121.54 133.29 -11.75 1.91e+00 2.74e-01 3.79e+01 angle pdb=" N THR B 71 " pdb=" CA THR B 71 " pdb=" C THR B 71 " ideal model delta sigma weight residual 109.81 121.90 -12.09 2.21e+00 2.05e-01 2.99e+01 angle pdb=" C08 HNX B 601 " pdb=" C09 HNX B 601 " pdb=" C10 HNX B 601 " ideal model delta sigma weight residual 111.98 126.75 -14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" C THR B 299 " ideal model delta sigma weight residual 114.62 109.03 5.59 1.14e+00 7.69e-01 2.40e+01 angle pdb=" C VAL B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta sigma weight residual 122.74 129.75 -7.01 1.44e+00 4.82e-01 2.37e+01 ... (remaining 10483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 4514 33.93 - 67.86: 141 67.86 - 101.79: 34 101.79 - 135.72: 33 135.72 - 169.66: 11 Dihedral angle restraints: 4733 sinusoidal: 2053 harmonic: 2680 Sorted by residual: dihedral pdb=" CA LEU B 137 " pdb=" C LEU B 137 " pdb=" N LEU B 138 " pdb=" CA LEU B 138 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PRO A 209 " pdb=" C PRO A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CAD Y01 B 603 " pdb=" CAZ Y01 B 603 " pdb=" CBH Y01 B 603 " pdb=" CAV Y01 B 603 " ideal model delta sinusoidal sigma weight residual 288.69 119.03 169.66 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.191: 1223 1.191 - 2.381: 0 2.381 - 3.572: 0 3.572 - 4.763: 0 4.763 - 5.954: 10 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CBI Y01 B 602 " pdb=" CAU Y01 B 602 " pdb=" CBE Y01 B 602 " pdb=" CBG Y01 B 602 " both_signs ideal model delta sigma weight residual False 2.94 -3.02 5.95 2.00e-01 2.50e+01 8.86e+02 chirality pdb=" CBI Y01 B 603 " pdb=" CAU Y01 B 603 " pdb=" CBE Y01 B 603 " pdb=" CBG Y01 B 603 " both_signs ideal model delta sigma weight residual False 2.94 -2.96 5.90 2.00e-01 2.50e+01 8.71e+02 chirality pdb=" CBH Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CAZ Y01 B 602 " pdb=" CBF Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.85 2.64 -5.49 2.00e-01 2.50e+01 7.55e+02 ... (remaining 1230 not shown) Planarity restraints: 1285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 137 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C LEU B 137 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU B 137 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU B 138 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 282 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO B 283 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 469 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO B 470 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.034 5.00e-02 4.00e+02 ... (remaining 1282 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 57 2.56 - 3.14: 5470 3.14 - 3.73: 11392 3.73 - 4.31: 15995 4.31 - 4.90: 26576 Nonbonded interactions: 59490 Sorted by model distance: nonbonded pdb=" OE1 GLU B 506 " pdb=" N THR B 507 " model vdw 1.969 3.120 nonbonded pdb=" O GLY B 67 " pdb=" OG1 THR B 71 " model vdw 2.279 3.040 nonbonded pdb=" O ASP A 325 " pdb=" OG1 THR A 329 " model vdw 2.291 3.040 nonbonded pdb=" O TYR A 251 " pdb=" OG SER A 254 " model vdw 2.300 3.040 nonbonded pdb=" O ILE B 139 " pdb=" OG SER B 143 " model vdw 2.309 3.040 ... (remaining 59485 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.160 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.011 0.225 7701 Z= 0.663 Angle : 1.122 14.771 10488 Z= 0.580 Chirality : 0.490 5.954 1233 Planarity : 0.007 0.071 1281 Dihedral : 23.271 169.655 3008 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.16 % Favored : 91.30 % Rotamer: Outliers : 0.63 % Allowed : 5.45 % Favored : 93.92 % 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: -3.42 (0.22), residues: 931 helix: -1.97 (0.18), residues: 485 sheet: -1.34 (0.61), residues: 65 loop : -2.73 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 220 HIS 0.004 0.001 HIS B 367 PHE 0.017 0.002 PHE A 627 TYR 0.014 0.002 TYR B 387 ARG 0.002 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8282 (pttm) cc_final: 0.7927 (mtmt) REVERT: B 77 LYS cc_start: 0.8421 (tppt) cc_final: 0.7895 (mmtm) REVERT: B 81 SER cc_start: 0.8881 (p) cc_final: 0.8660 (p) REVERT: B 238 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5821 (pt) REVERT: B 365 MET cc_start: 0.8943 (mtt) cc_final: 0.8591 (mtt) outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 1.0332 time to fit residues: 134.9835 Evaluate side-chains 79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 506 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 340 GLN A 353 ASN A 539 HIS A 557 HIS A 580 GLN B 273 ASN B 358 HIS ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.082644 restraints weight = 12670.715| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.94 r_work: 0.2876 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7701 Z= 0.185 Angle : 1.229 32.933 10488 Z= 0.483 Chirality : 0.111 1.853 1233 Planarity : 0.005 0.044 1281 Dihedral : 24.284 179.534 1373 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.41 % Favored : 92.16 % Rotamer: Outliers : 1.65 % Allowed : 12.55 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.32 (0.27), residues: 931 helix: 0.22 (0.22), residues: 498 sheet: -1.08 (0.60), residues: 69 loop : -2.40 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS A 620 PHE 0.018 0.001 PHE B 462 TYR 0.012 0.001 TYR A 629 ARG 0.006 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7314 (t70) cc_final: 0.6981 (t0) REVERT: A 575 LEU cc_start: 0.8822 (mp) cc_final: 0.8607 (mt) REVERT: B 77 LYS cc_start: 0.8287 (tppt) cc_final: 0.7971 (ttpp) REVERT: B 218 GLN cc_start: 0.7848 (tp40) cc_final: 0.7495 (tm-30) REVERT: B 451 PHE cc_start: 0.7714 (m-80) cc_final: 0.7455 (m-10) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 0.8022 time to fit residues: 82.7196 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 HIS ** 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 = 0.3491 r_free = 0.3491 target = 0.113101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.082174 restraints weight = 12786.126| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.93 r_work: 0.2860 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7701 Z= 0.196 Angle : 1.181 31.110 10488 Z= 0.455 Chirality : 0.111 1.877 1233 Planarity : 0.004 0.040 1281 Dihedral : 23.580 179.737 1364 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.73 % Favored : 92.05 % Rotamer: Outliers : 3.42 % Allowed : 12.67 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 931 helix: 1.15 (0.24), residues: 499 sheet: -0.92 (0.60), residues: 69 loop : -2.14 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.002 0.001 HIS A 620 PHE 0.021 0.001 PHE B 462 TYR 0.018 0.001 TYR A 629 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7476 (t70) cc_final: 0.7097 (t0) REVERT: A 499 ASP cc_start: 0.7985 (p0) cc_final: 0.7763 (t0) REVERT: A 562 GLU cc_start: 0.8160 (tp30) cc_final: 0.7789 (tp30) REVERT: B 77 LYS cc_start: 0.8235 (tppt) cc_final: 0.7925 (ttpp) REVERT: B 218 GLN cc_start: 0.7729 (tp40) cc_final: 0.7430 (tm-30) REVERT: B 394 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: B 451 PHE cc_start: 0.7711 (m-80) cc_final: 0.7510 (m-10) outliers start: 27 outliers final: 9 residues processed: 101 average time/residue: 0.8637 time to fit residues: 94.6920 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 394 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 0.0170 chunk 88 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 HIS ** 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 = 0.3552 r_free = 0.3552 target = 0.116707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085836 restraints weight = 12679.345| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.89 r_work: 0.2925 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7701 Z= 0.164 Angle : 1.168 30.905 10488 Z= 0.442 Chirality : 0.110 1.825 1233 Planarity : 0.004 0.039 1281 Dihedral : 23.236 178.401 1364 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.52 % Favored : 92.27 % Rotamer: Outliers : 1.90 % Allowed : 14.83 % Favored : 83.27 % 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: 0.13 (0.28), residues: 931 helix: 1.59 (0.24), residues: 499 sheet: -0.79 (0.58), residues: 72 loop : -1.98 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 420 PHE 0.008 0.001 PHE B 95 TYR 0.009 0.001 TYR A 226 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.897 Fit side-chains REVERT: A 398 ASP cc_start: 0.7418 (t70) cc_final: 0.7100 (t0) REVERT: A 562 GLU cc_start: 0.8105 (tp30) cc_final: 0.7846 (tp30) REVERT: B 77 LYS cc_start: 0.8308 (tppt) cc_final: 0.8016 (ttpp) REVERT: B 218 GLN cc_start: 0.7704 (tp40) cc_final: 0.7393 (tm-30) REVERT: B 394 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.6943 (m-80) outliers start: 15 outliers final: 6 residues processed: 101 average time/residue: 0.8067 time to fit residues: 88.7376 Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.085512 restraints weight = 12608.673| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.87 r_work: 0.2912 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7701 Z= 0.182 Angle : 1.175 31.048 10488 Z= 0.448 Chirality : 0.111 1.834 1233 Planarity : 0.004 0.038 1281 Dihedral : 23.000 179.096 1362 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.06 % Favored : 91.84 % Rotamer: Outliers : 2.15 % Allowed : 16.86 % Favored : 80.99 % 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: 0.43 (0.29), residues: 931 helix: 1.99 (0.24), residues: 486 sheet: -0.74 (0.57), residues: 72 loop : -1.93 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS B 367 PHE 0.020 0.001 PHE B 462 TYR 0.010 0.001 TYR A 554 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.871 Fit side-chains REVERT: A 398 ASP cc_start: 0.7504 (t70) cc_final: 0.7193 (t0) REVERT: A 562 GLU cc_start: 0.8024 (tp30) cc_final: 0.7819 (tp30) REVERT: B 77 LYS cc_start: 0.8315 (tppt) cc_final: 0.8062 (ttpp) REVERT: B 218 GLN cc_start: 0.7756 (tp40) cc_final: 0.7453 (tm-30) REVERT: B 394 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: B 451 PHE cc_start: 0.7684 (m-10) cc_final: 0.7356 (m-10) outliers start: 17 outliers final: 9 residues processed: 89 average time/residue: 0.7449 time to fit residues: 73.0527 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.0370 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.0030 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 0.0020 chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.087845 restraints weight = 12573.009| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.91 r_work: 0.2950 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7701 Z= 0.154 Angle : 1.161 30.837 10488 Z= 0.436 Chirality : 0.111 1.841 1233 Planarity : 0.004 0.037 1281 Dihedral : 22.723 179.393 1362 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.80 % Rotamer: Outliers : 2.15 % Allowed : 17.36 % Favored : 80.48 % 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: 0.71 (0.29), residues: 931 helix: 2.26 (0.24), residues: 485 sheet: -0.69 (0.57), residues: 72 loop : -1.83 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 PHE 0.009 0.001 PHE B 330 TYR 0.007 0.001 TYR A 226 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7462 (t70) cc_final: 0.7131 (t0) REVERT: A 562 GLU cc_start: 0.8106 (tp30) cc_final: 0.7776 (tp30) REVERT: B 77 LYS cc_start: 0.8339 (tppt) cc_final: 0.8099 (ttpp) REVERT: B 218 GLN cc_start: 0.7698 (tp40) cc_final: 0.7431 (tm-30) REVERT: B 394 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: B 451 PHE cc_start: 0.7659 (m-10) cc_final: 0.7323 (m-10) outliers start: 17 outliers final: 10 residues processed: 96 average time/residue: 0.8047 time to fit residues: 84.6917 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 480 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.0030 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 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 = 0.3549 r_free = 0.3549 target = 0.116120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.085246 restraints weight = 12689.271| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.89 r_work: 0.2914 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7701 Z= 0.191 Angle : 1.174 31.121 10488 Z= 0.443 Chirality : 0.111 1.838 1233 Planarity : 0.004 0.038 1281 Dihedral : 22.646 179.675 1362 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 2.92 % Allowed : 16.73 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.29), residues: 931 helix: 2.28 (0.24), residues: 487 sheet: -0.73 (0.57), residues: 72 loop : -1.75 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 220 HIS 0.003 0.001 HIS B 367 PHE 0.019 0.001 PHE B 462 TYR 0.011 0.001 TYR A 554 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 163 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7836 (m) REVERT: A 171 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8415 (pt) REVERT: A 398 ASP cc_start: 0.7531 (t70) cc_final: 0.7179 (t0) REVERT: A 562 GLU cc_start: 0.8071 (tp30) cc_final: 0.7722 (tp30) REVERT: B 77 LYS cc_start: 0.8350 (tppt) cc_final: 0.8109 (ttpp) REVERT: B 218 GLN cc_start: 0.7741 (tp40) cc_final: 0.7474 (tm-30) REVERT: B 305 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7770 (mtm) REVERT: B 394 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: B 451 PHE cc_start: 0.7735 (m-10) cc_final: 0.7362 (m-10) outliers start: 23 outliers final: 13 residues processed: 91 average time/residue: 0.6904 time to fit residues: 69.5868 Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 480 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 2.9990 chunk 34 optimal weight: 0.0270 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 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 = 0.3569 r_free = 0.3569 target = 0.117625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.086735 restraints weight = 12788.775| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.91 r_work: 0.2943 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7701 Z= 0.157 Angle : 1.168 30.925 10488 Z= 0.438 Chirality : 0.111 1.842 1233 Planarity : 0.004 0.037 1281 Dihedral : 22.534 179.635 1362 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.80 % Rotamer: Outliers : 2.92 % Allowed : 16.86 % Favored : 80.23 % 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: 0.90 (0.29), residues: 931 helix: 2.40 (0.24), residues: 487 sheet: -0.71 (0.56), residues: 72 loop : -1.71 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 PHE 0.013 0.001 PHE B 330 TYR 0.009 0.001 TYR A 554 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 163 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7878 (m) REVERT: A 171 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8428 (pt) REVERT: A 398 ASP cc_start: 0.7475 (t70) cc_final: 0.7122 (t0) REVERT: A 562 GLU cc_start: 0.8070 (tp30) cc_final: 0.7727 (tp30) REVERT: B 77 LYS cc_start: 0.8345 (tppt) cc_final: 0.8119 (ttpp) REVERT: B 218 GLN cc_start: 0.7726 (tp40) cc_final: 0.7445 (tm-30) REVERT: B 305 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7733 (mtm) REVERT: B 387 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 394 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: B 451 PHE cc_start: 0.7716 (m-10) cc_final: 0.7325 (m-10) outliers start: 23 outliers final: 10 residues processed: 91 average time/residue: 0.7164 time to fit residues: 72.0332 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 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 = 0.3539 r_free = 0.3539 target = 0.115582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084560 restraints weight = 12892.765| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.93 r_work: 0.2906 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7701 Z= 0.198 Angle : 1.169 31.114 10488 Z= 0.442 Chirality : 0.111 1.837 1233 Planarity : 0.004 0.038 1281 Dihedral : 22.493 179.669 1362 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.30 % Favored : 92.59 % Rotamer: Outliers : 2.28 % Allowed : 17.36 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.29), residues: 931 helix: 2.35 (0.24), residues: 486 sheet: -0.75 (0.57), residues: 72 loop : -1.72 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.003 0.001 HIS B 367 PHE 0.020 0.001 PHE B 462 TYR 0.011 0.001 TYR A 554 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 163 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7880 (m) REVERT: A 171 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8437 (pt) REVERT: A 398 ASP cc_start: 0.7514 (t70) cc_final: 0.7160 (t0) REVERT: A 562 GLU cc_start: 0.8070 (tp30) cc_final: 0.7789 (tp30) REVERT: B 77 LYS cc_start: 0.8347 (tppt) cc_final: 0.8122 (ttpp) REVERT: B 218 GLN cc_start: 0.7753 (tp40) cc_final: 0.7468 (tm-30) REVERT: B 394 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: B 451 PHE cc_start: 0.7795 (m-10) cc_final: 0.7406 (m-10) outliers start: 18 outliers final: 10 residues processed: 88 average time/residue: 0.6969 time to fit residues: 67.7149 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 42 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 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 = 0.3555 r_free = 0.3555 target = 0.116751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.086047 restraints weight = 12720.475| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.91 r_work: 0.2928 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7701 Z= 0.166 Angle : 1.163 31.011 10488 Z= 0.439 Chirality : 0.111 1.842 1233 Planarity : 0.004 0.037 1281 Dihedral : 22.427 179.976 1362 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.30 % Favored : 92.59 % Rotamer: Outliers : 1.90 % Allowed : 18.00 % Favored : 80.10 % 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: 0.87 (0.29), residues: 931 helix: 2.34 (0.24), residues: 488 sheet: -0.77 (0.57), residues: 72 loop : -1.66 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 PHE 0.018 0.001 PHE B 330 TYR 0.008 0.001 TYR A 554 ARG 0.002 0.000 ARG A 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 163 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7793 (m) REVERT: A 171 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8480 (pt) REVERT: A 172 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7756 (ptpp) REVERT: A 398 ASP cc_start: 0.7478 (t70) cc_final: 0.7133 (t0) REVERT: A 562 GLU cc_start: 0.8080 (tp30) cc_final: 0.7755 (tp30) REVERT: B 77 LYS cc_start: 0.8461 (tppt) cc_final: 0.8240 (ttpp) REVERT: B 394 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: B 451 PHE cc_start: 0.7748 (m-10) cc_final: 0.7346 (m-10) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.7287 time to fit residues: 66.0753 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 59 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 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 = 0.3571 r_free = 0.3571 target = 0.117872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087200 restraints weight = 12779.830| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.92 r_work: 0.2955 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7701 Z= 0.157 Angle : 1.156 30.987 10488 Z= 0.435 Chirality : 0.111 1.845 1233 Planarity : 0.004 0.038 1281 Dihedral : 22.325 179.682 1362 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.28 % Allowed : 17.87 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 931 helix: 2.39 (0.24), residues: 488 sheet: -0.82 (0.57), residues: 72 loop : -1.63 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 PHE 0.022 0.001 PHE B 330 TYR 0.007 0.001 TYR A 554 ARG 0.002 0.000 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4170.47 seconds wall clock time: 74 minutes 34.24 seconds (4474.24 seconds total)