Starting phenix.real_space_refine on Sun Apr 5 04:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsk_30835/04_2026/7dsk_30835_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsk_30835/04_2026/7dsk_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 { model { file = "/net/cci-nas-00/data/ceres_data/7dsk_30835/04_2026/7dsk_30835_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsk_30835/04_2026/7dsk_30835_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dsk_30835/04_2026/7dsk_30835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsk_30835/04_2026/7dsk_30835.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/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: 1.91, per 1000 atoms: 0.25 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: 0.83 Conformation dependent library (CDL) restraints added in 285.1 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: 0.22 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: 0.91 Time building geometry restraints manager: 1.03 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.850 Find NCS groups from input model: 0.060 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.390 ------------------------------------------------------------------------------- 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 7710 Z= 0.519 Angle : 1.139 14.771 10514 Z= 0.584 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 : 5.13 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG B 141 TYR 0.014 0.002 TYR B 387 PHE 0.017 0.002 PHE A 627 TRP 0.012 0.001 TRP A 220 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.01053 ( 7701) covalent geometry : angle 1.12151 (10488) SS BOND : bond 0.00040 ( 1) SS BOND : angle 5.00964 ( 2) hydrogen bonds : bond 0.18583 ( 376) hydrogen bonds : angle 6.69292 ( 1083) link_BETA1-4 : bond 0.01247 ( 4) link_BETA1-4 : angle 3.95375 ( 12) link_NAG-ASN : bond 0.00317 ( 4) link_NAG-ASN : angle 4.15950 ( 12) *********************** 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 : 0.267 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: 0.4740 time to fit residues: 61.6934 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 : 0.250 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 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 217 GLN A 340 GLN A 353 ASN A 539 HIS A 557 HIS A 580 GLN B 273 ASN B 358 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081837 restraints weight = 12824.704| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.96 r_work: 0.2860 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7710 Z= 0.143 Angle : 1.248 33.015 10514 Z= 0.492 Chirality : 0.108 1.798 1233 Planarity : 0.005 0.047 1281 Dihedral : 24.259 177.596 1373 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.30 % Favored : 92.27 % Rotamer: Outliers : 1.52 % Allowed : 12.80 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.26), residues: 931 helix: 0.13 (0.22), residues: 501 sheet: -1.38 (0.57), residues: 71 loop : -2.45 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.012 0.001 TYR A 629 PHE 0.019 0.001 PHE B 462 TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7701) covalent geometry : angle 1.24054 (10488) SS BOND : bond 0.00956 ( 1) SS BOND : angle 5.13287 ( 2) hydrogen bonds : bond 0.05521 ( 376) hydrogen bonds : angle 4.40544 ( 1083) link_BETA1-4 : bond 0.00812 ( 4) link_BETA1-4 : angle 2.13095 ( 12) link_NAG-ASN : bond 0.00198 ( 4) link_NAG-ASN : angle 3.15424 ( 12) *********************** 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 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.223 Fit side-chains REVERT: A 398 ASP cc_start: 0.7357 (t70) cc_final: 0.7043 (t0) REVERT: B 77 LYS cc_start: 0.8287 (tppt) cc_final: 0.7964 (ttpp) REVERT: B 365 MET cc_start: 0.9191 (mtt) cc_final: 0.8831 (mtt) REVERT: B 415 MET cc_start: 0.8250 (tmm) cc_final: 0.8043 (ttt) REVERT: B 451 PHE cc_start: 0.7753 (m-80) cc_final: 0.7517 (m-10) outliers start: 12 outliers final: 5 residues processed: 91 average time/residue: 0.3555 time to fit residues: 35.1873 Evaluate side-chains 78 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 32 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 0.0030 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.111942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.081045 restraints weight = 12741.795| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.92 r_work: 0.2835 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7710 Z= 0.147 Angle : 1.201 31.197 10514 Z= 0.463 Chirality : 0.111 1.837 1233 Planarity : 0.004 0.041 1281 Dihedral : 23.603 179.902 1362 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.52 % Favored : 92.16 % Rotamer: Outliers : 3.30 % Allowed : 13.05 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.28), residues: 931 helix: 1.18 (0.23), residues: 494 sheet: -1.09 (0.58), residues: 72 loop : -2.19 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.017 0.001 TYR A 629 PHE 0.021 0.001 PHE B 462 TRP 0.010 0.001 TRP A 220 HIS 0.003 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7701) covalent geometry : angle 1.19566 (10488) SS BOND : bond 0.00259 ( 1) SS BOND : angle 3.31406 ( 2) hydrogen bonds : bond 0.05182 ( 376) hydrogen bonds : angle 4.12797 ( 1083) link_BETA1-4 : bond 0.00852 ( 4) link_BETA1-4 : angle 2.10364 ( 12) link_NAG-ASN : bond 0.00100 ( 4) link_NAG-ASN : angle 2.77852 ( 12) *********************** 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 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.262 Fit side-chains REVERT: A 398 ASP cc_start: 0.7427 (t70) cc_final: 0.7081 (t0) REVERT: A 499 ASP cc_start: 0.8010 (p0) cc_final: 0.7769 (t0) REVERT: A 562 GLU cc_start: 0.8176 (tp30) cc_final: 0.7821 (tp30) REVERT: B 77 LYS cc_start: 0.8238 (tppt) cc_final: 0.7938 (ttpp) REVERT: B 218 GLN cc_start: 0.7767 (tp40) cc_final: 0.7442 (tm-30) REVERT: B 303 GLU cc_start: 0.8447 (pt0) cc_final: 0.7990 (tp30) REVERT: B 394 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: B 451 PHE cc_start: 0.7747 (m-80) cc_final: 0.7536 (m-10) outliers start: 26 outliers final: 11 residues processed: 96 average time/residue: 0.3764 time to fit residues: 39.2335 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 203 VAL 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 217 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 480 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 40 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.114748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083738 restraints weight = 12838.699| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.90 r_work: 0.2894 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7710 Z= 0.130 Angle : 1.185 31.066 10514 Z= 0.451 Chirality : 0.110 1.818 1233 Planarity : 0.004 0.041 1281 Dihedral : 23.290 178.775 1362 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.84 % Favored : 91.84 % Rotamer: Outliers : 2.28 % Allowed : 14.32 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.29), residues: 931 helix: 1.63 (0.24), residues: 494 sheet: -0.82 (0.58), residues: 72 loop : -2.00 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.010 0.001 TYR A 629 PHE 0.009 0.001 PHE B 95 TRP 0.009 0.001 TRP A 220 HIS 0.002 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7701) covalent geometry : angle 1.17992 (10488) SS BOND : bond 0.00754 ( 1) SS BOND : angle 3.02447 ( 2) hydrogen bonds : bond 0.04729 ( 376) hydrogen bonds : angle 3.96311 ( 1083) link_BETA1-4 : bond 0.00680 ( 4) link_BETA1-4 : angle 2.26178 ( 12) link_NAG-ASN : bond 0.00106 ( 4) link_NAG-ASN : angle 2.71638 ( 12) *********************** 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 98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.302 Fit side-chains REVERT: A 398 ASP cc_start: 0.7549 (t70) cc_final: 0.7191 (t0) REVERT: A 562 GLU cc_start: 0.8106 (tp30) cc_final: 0.7845 (tp30) REVERT: B 77 LYS cc_start: 0.8312 (tppt) cc_final: 0.8028 (ttpp) REVERT: B 218 GLN cc_start: 0.7786 (tp40) cc_final: 0.7447 (tm-30) REVERT: B 303 GLU cc_start: 0.8449 (pt0) cc_final: 0.8066 (tp30) REVERT: B 394 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.6932 (m-80) outliers start: 18 outliers final: 9 residues processed: 93 average time/residue: 0.3788 time to fit residues: 38.2695 Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP 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 206 LEU Chi-restraints excluded: chain B residue 236 THR 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 64 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.114223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.083408 restraints weight = 12762.646| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.87 r_work: 0.2885 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7710 Z= 0.136 Angle : 1.186 31.194 10514 Z= 0.451 Chirality : 0.111 1.829 1233 Planarity : 0.004 0.040 1281 Dihedral : 23.066 179.131 1362 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.38 % Favored : 91.51 % Rotamer: Outliers : 2.28 % Allowed : 16.60 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.29), residues: 931 helix: 1.83 (0.24), residues: 495 sheet: -0.81 (0.58), residues: 72 loop : -1.87 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.012 0.001 TYR A 629 PHE 0.020 0.001 PHE B 462 TRP 0.008 0.001 TRP A 220 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7701) covalent geometry : angle 1.18043 (10488) SS BOND : bond 0.00686 ( 1) SS BOND : angle 2.74161 ( 2) hydrogen bonds : bond 0.04762 ( 376) hydrogen bonds : angle 3.92726 ( 1083) link_BETA1-4 : bond 0.00905 ( 4) link_BETA1-4 : angle 2.37427 ( 12) link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 2.72617 ( 12) *********************** 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 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.290 Fit side-chains REVERT: A 398 ASP cc_start: 0.7607 (t70) cc_final: 0.7250 (t0) REVERT: A 562 GLU cc_start: 0.8047 (tp30) cc_final: 0.7811 (tp30) REVERT: B 77 LYS cc_start: 0.8318 (tppt) cc_final: 0.8044 (ttpp) REVERT: B 218 GLN cc_start: 0.7759 (tp40) cc_final: 0.7425 (tm-30) REVERT: B 303 GLU cc_start: 0.8409 (pt0) cc_final: 0.8178 (pm20) REVERT: B 394 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.6907 (m-80) REVERT: B 451 PHE cc_start: 0.7626 (m-10) cc_final: 0.7286 (m-10) outliers start: 18 outliers final: 9 residues processed: 89 average time/residue: 0.4138 time to fit residues: 39.8534 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP 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 206 LEU Chi-restraints excluded: chain B residue 236 THR 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 25 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.115263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.084488 restraints weight = 12662.612| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.87 r_work: 0.2902 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7710 Z= 0.125 Angle : 1.178 31.013 10514 Z= 0.447 Chirality : 0.111 1.829 1233 Planarity : 0.004 0.039 1281 Dihedral : 22.847 178.844 1362 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 2.15 % Allowed : 16.98 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.29), residues: 931 helix: 2.02 (0.24), residues: 493 sheet: -0.67 (0.58), residues: 72 loop : -1.86 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.010 0.001 TYR A 554 PHE 0.012 0.001 PHE B 330 TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7701) covalent geometry : angle 1.17227 (10488) SS BOND : bond 0.00178 ( 1) SS BOND : angle 2.59274 ( 2) hydrogen bonds : bond 0.04417 ( 376) hydrogen bonds : angle 3.83603 ( 1083) link_BETA1-4 : bond 0.00769 ( 4) link_BETA1-4 : angle 2.45130 ( 12) link_NAG-ASN : bond 0.00116 ( 4) link_NAG-ASN : angle 2.74067 ( 12) *********************** 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 : 0.291 Fit side-chains REVERT: A 398 ASP cc_start: 0.7609 (t70) cc_final: 0.7240 (t0) REVERT: A 562 GLU cc_start: 0.8031 (tp30) cc_final: 0.7739 (tp30) REVERT: B 77 LYS cc_start: 0.8321 (tppt) cc_final: 0.8080 (ttpp) REVERT: B 218 GLN cc_start: 0.7719 (tp40) cc_final: 0.7437 (tm-30) REVERT: B 303 GLU cc_start: 0.8416 (pt0) cc_final: 0.8190 (pm20) REVERT: B 394 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: B 451 PHE cc_start: 0.7655 (m-10) cc_final: 0.7297 (m-10) outliers start: 17 outliers final: 11 residues processed: 96 average time/residue: 0.3437 time to fit residues: 36.0809 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain B residue 282 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 0.0040 chunk 33 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.4154 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.112430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081452 restraints weight = 12900.353| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.90 r_work: 0.2851 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7710 Z= 0.172 Angle : 1.201 31.393 10514 Z= 0.461 Chirality : 0.111 1.818 1233 Planarity : 0.004 0.043 1281 Dihedral : 22.788 179.344 1362 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.16 % Favored : 91.73 % Rotamer: Outliers : 2.66 % Allowed : 17.87 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.29), residues: 931 helix: 1.94 (0.24), residues: 494 sheet: -0.79 (0.57), residues: 72 loop : -1.82 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.013 0.001 TYR A 629 PHE 0.021 0.001 PHE B 462 TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7701) covalent geometry : angle 1.19507 (10488) SS BOND : bond 0.00053 ( 1) SS BOND : angle 3.40706 ( 2) hydrogen bonds : bond 0.05263 ( 376) hydrogen bonds : angle 3.99424 ( 1083) link_BETA1-4 : bond 0.00734 ( 4) link_BETA1-4 : angle 2.44866 ( 12) link_NAG-ASN : bond 0.00096 ( 4) link_NAG-ASN : angle 2.76151 ( 12) *********************** 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 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8080 (ptpp) REVERT: A 562 GLU cc_start: 0.8103 (tp30) cc_final: 0.7769 (tp30) REVERT: B 77 LYS cc_start: 0.8325 (tppt) cc_final: 0.8085 (ttpp) REVERT: B 218 GLN cc_start: 0.7883 (tp40) cc_final: 0.7515 (tm-30) REVERT: B 303 GLU cc_start: 0.8516 (pt0) cc_final: 0.8265 (pm20) REVERT: B 394 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: B 415 MET cc_start: 0.8311 (ttt) cc_final: 0.8089 (ttt) REVERT: B 451 PHE cc_start: 0.7766 (m-10) cc_final: 0.7435 (m-10) outliers start: 21 outliers final: 13 residues processed: 89 average time/residue: 0.3533 time to fit residues: 34.4271 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 137 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 236 THR Chi-restraints excluded: chain B residue 282 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.112836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.081782 restraints weight = 12973.313| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.91 r_work: 0.2862 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7710 Z= 0.160 Angle : 1.198 31.309 10514 Z= 0.459 Chirality : 0.110 1.819 1233 Planarity : 0.004 0.042 1281 Dihedral : 22.706 179.014 1362 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 2.79 % Allowed : 18.00 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.29), residues: 931 helix: 2.02 (0.24), residues: 492 sheet: -0.70 (0.58), residues: 72 loop : -1.81 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.012 0.001 TYR A 554 PHE 0.011 0.001 PHE B 330 TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7701) covalent geometry : angle 1.19215 (10488) SS BOND : bond 0.00159 ( 1) SS BOND : angle 3.21660 ( 2) hydrogen bonds : bond 0.05107 ( 376) hydrogen bonds : angle 3.98424 ( 1083) link_BETA1-4 : bond 0.00762 ( 4) link_BETA1-4 : angle 2.41180 ( 12) link_NAG-ASN : bond 0.00090 ( 4) link_NAG-ASN : angle 2.75099 ( 12) *********************** 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 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 562 GLU cc_start: 0.8104 (tp30) cc_final: 0.7802 (tp30) REVERT: B 51 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.8019 (t) REVERT: B 77 LYS cc_start: 0.8441 (tppt) cc_final: 0.8208 (ttpp) REVERT: B 218 GLN cc_start: 0.7900 (tp40) cc_final: 0.7549 (tm-30) REVERT: B 303 GLU cc_start: 0.8535 (pt0) cc_final: 0.8276 (pm20) REVERT: B 305 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7819 (mtm) REVERT: B 394 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: B 451 PHE cc_start: 0.7857 (m-10) cc_final: 0.7497 (m-10) outliers start: 22 outliers final: 16 residues processed: 85 average time/residue: 0.3604 time to fit residues: 33.4738 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 282 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.0030 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.0050 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.116539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.085520 restraints weight = 12786.242| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.95 r_work: 0.2911 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7710 Z= 0.117 Angle : 1.173 31.100 10514 Z= 0.446 Chirality : 0.111 1.833 1233 Planarity : 0.004 0.042 1281 Dihedral : 22.558 179.907 1362 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.52 % Favored : 92.37 % Rotamer: Outliers : 2.03 % Allowed : 18.88 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.29), residues: 931 helix: 2.25 (0.24), residues: 491 sheet: -0.65 (0.57), residues: 72 loop : -1.74 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.008 0.001 TYR A 226 PHE 0.022 0.001 PHE B 462 TRP 0.010 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7701) covalent geometry : angle 1.16772 (10488) SS BOND : bond 0.00002 ( 1) SS BOND : angle 2.50900 ( 2) hydrogen bonds : bond 0.04030 ( 376) hydrogen bonds : angle 3.77971 ( 1083) link_BETA1-4 : bond 0.00792 ( 4) link_BETA1-4 : angle 2.37106 ( 12) link_NAG-ASN : bond 0.00178 ( 4) link_NAG-ASN : angle 2.80965 ( 12) *********************** 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: 16 poor density : 78 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 562 GLU cc_start: 0.8093 (tp30) cc_final: 0.7736 (tp30) REVERT: B 77 LYS cc_start: 0.8430 (tppt) cc_final: 0.8219 (ttpp) REVERT: B 218 GLN cc_start: 0.7751 (tp40) cc_final: 0.7462 (tm-30) REVERT: B 303 GLU cc_start: 0.8529 (pt0) cc_final: 0.8297 (pm20) REVERT: B 394 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: B 451 PHE cc_start: 0.7780 (m-10) cc_final: 0.7410 (m-10) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.3227 time to fit residues: 31.8147 Evaluate side-chains 82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain B residue 45 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.115919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.085014 restraints weight = 12681.441| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.93 r_work: 0.2923 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7710 Z= 0.122 Angle : 1.181 31.098 10514 Z= 0.449 Chirality : 0.111 1.836 1233 Planarity : 0.004 0.041 1281 Dihedral : 22.490 179.792 1362 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 1.27 % Allowed : 19.77 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.29), residues: 931 helix: 2.24 (0.24), residues: 492 sheet: -0.71 (0.57), residues: 72 loop : -1.70 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.009 0.001 TYR A 554 PHE 0.021 0.001 PHE B 330 TRP 0.008 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7701) covalent geometry : angle 1.17536 (10488) SS BOND : bond 0.00051 ( 1) SS BOND : angle 2.58535 ( 2) hydrogen bonds : bond 0.04192 ( 376) hydrogen bonds : angle 3.79153 ( 1083) link_BETA1-4 : bond 0.00755 ( 4) link_BETA1-4 : angle 2.32137 ( 12) link_NAG-ASN : bond 0.00162 ( 4) link_NAG-ASN : angle 2.84376 ( 12) ********************** 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 82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 562 GLU cc_start: 0.8094 (tp30) cc_final: 0.7731 (tp30) REVERT: B 77 LYS cc_start: 0.8431 (tppt) cc_final: 0.8224 (ttpp) REVERT: B 218 GLN cc_start: 0.7768 (tp40) cc_final: 0.7460 (tm-30) REVERT: B 394 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6700 (m-80) REVERT: B 451 PHE cc_start: 0.7812 (m-10) cc_final: 0.7437 (m-10) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.3334 time to fit residues: 30.1808 Evaluate side-chains 80 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain B residue 45 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 66 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.113980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.083021 restraints weight = 12713.124| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.90 r_work: 0.2880 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7710 Z= 0.147 Angle : 1.188 31.264 10514 Z= 0.455 Chirality : 0.111 1.829 1233 Planarity : 0.004 0.044 1281 Dihedral : 22.447 179.666 1362 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 1.39 % Allowed : 20.03 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.29), residues: 931 helix: 2.19 (0.24), residues: 492 sheet: -0.75 (0.57), residues: 72 loop : -1.67 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.011 0.001 TYR A 554 PHE 0.020 0.001 PHE B 462 TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7701) covalent geometry : angle 1.18184 (10488) SS BOND : bond 0.00078 ( 1) SS BOND : angle 2.90926 ( 2) hydrogen bonds : bond 0.04744 ( 376) hydrogen bonds : angle 3.90061 ( 1083) link_BETA1-4 : bond 0.00663 ( 4) link_BETA1-4 : angle 2.29589 ( 12) link_NAG-ASN : bond 0.00112 ( 4) link_NAG-ASN : angle 2.84738 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.65 seconds wall clock time: 35 minutes 14.53 seconds (2114.53 seconds total)