Starting phenix.real_space_refine on Mon Apr 28 10:53:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kju_62377/04_2025/9kju_62377_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kju_62377/04_2025/9kju_62377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kju_62377/04_2025/9kju_62377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kju_62377/04_2025/9kju_62377.map" model { file = "/net/cci-nas-00/data/ceres_data/9kju_62377/04_2025/9kju_62377_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kju_62377/04_2025/9kju_62377_neut.cif" } resolution = 2.7 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4821 2.51 5 N 1203 2.21 5 O 1348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7398 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: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3603 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 20, 'TRANS': 443} 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: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.64 Number of scatterers: 7398 At special positions: 0 Unit cell: (82.612, 84.786, 125.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1348 8.00 N 1203 7.00 C 4821 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 151 " distance=2.02 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: 1.72 Conformation dependent library (CDL) restraints added in 901.0 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: 1728 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 61.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 179 through 206 Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.887A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.608A 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 256 removed outlier: 3.593A pdb=" N LEU A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.861A pdb=" N PHE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.593A pdb=" N ALA A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.851A 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 356 through 372 removed outlier: 3.522A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.672A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 460 removed outlier: 3.565A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.591A pdb=" N LEU A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.790A 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 'A' and resid 585 through 589 removed outlier: 3.890A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 51 Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.560A pdb=" N SER B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 68 through 98 removed outlier: 3.645A pdb=" N GLY B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 113 through 126 Processing helix chain 'B' and resid 126 through 144 removed outlier: 3.861A pdb=" N THR B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 176 removed outlier: 3.804A pdb=" N SER B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 209 removed outlier: 3.772A pdb=" N GLY B 180 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 239 removed outlier: 3.709A pdb=" N LEU B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 removed outlier: 4.065A pdb=" N THR B 249 " --> pdb=" O ASN B 246 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLU B 250 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 252 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 285 removed outlier: 3.779A pdb=" N LEU B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Proline residue: B 268 - end of helix removed outlier: 3.569A pdb=" N ASN B 278 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.551A pdb=" N ILE B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 Processing helix chain 'B' and resid 310 through 341 removed outlier: 3.733A pdb=" N ASN B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 358 through 373 Processing helix chain 'B' and resid 378 through 384 removed outlier: 3.808A pdb=" N ILE B 382 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 407 removed outlier: 3.618A pdb=" N TYR B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TRP B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.517A pdb=" N ILE B 422 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Proline residue: B 435 - end of helix Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.908A pdb=" N SER B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 460 removed outlier: 3.575A pdb=" N LEU B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 488 removed outlier: 3.601A pdb=" N ILE B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.515A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY A 345 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 260 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP A 308 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU A 262 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR A 226 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 7.124A pdb=" N GLN A 280 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.622A 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 'A' and resid 593 through 594 Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 352 393 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1814 1.33 - 1.45: 1550 1.45 - 1.57: 4173 1.57 - 1.69: 0 1.69 - 1.80: 38 Bond restraints: 7575 Sorted by residual: bond pdb=" N PRO A 481 " pdb=" CD PRO A 481 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.87e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C LEU A 480 " pdb=" N PRO A 481 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.51e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" C HIS A 539 " pdb=" N GLY A 540 " ideal model delta sigma weight residual 1.328 1.298 0.031 1.34e-02 5.57e+03 5.29e+00 ... (remaining 7570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 9954 2.54 - 5.08: 295 5.08 - 7.62: 38 7.62 - 10.16: 13 10.16 - 12.70: 2 Bond angle restraints: 10302 Sorted by residual: angle pdb=" N ASP A 272 " pdb=" CA ASP A 272 " pdb=" C ASP A 272 " ideal model delta sigma weight residual 109.59 100.37 9.22 1.47e+00 4.63e-01 3.93e+01 angle pdb=" N ARG B 288 " pdb=" CA ARG B 288 " pdb=" C ARG B 288 " ideal model delta sigma weight residual 111.28 115.88 -4.60 1.09e+00 8.42e-01 1.78e+01 angle pdb=" C LEU A 480 " pdb=" N PRO A 481 " pdb=" CA PRO A 481 " ideal model delta sigma weight residual 119.84 114.62 5.22 1.25e+00 6.40e-01 1.75e+01 angle pdb=" N ASP A 271 " pdb=" CA ASP A 271 " pdb=" C ASP A 271 " ideal model delta sigma weight residual 110.80 119.09 -8.29 2.13e+00 2.20e-01 1.52e+01 angle pdb=" CA ARG B 355 " pdb=" CB ARG B 355 " pdb=" CG ARG B 355 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 ... (remaining 10297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.48: 4162 20.48 - 40.96: 309 40.96 - 61.44: 55 61.44 - 81.92: 11 81.92 - 102.41: 12 Dihedral angle restraints: 4549 sinusoidal: 1856 harmonic: 2693 Sorted by residual: dihedral pdb=" CA VAL B 353 " pdb=" C VAL B 353 " pdb=" N GLU B 354 " pdb=" CA GLU B 354 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASN A 317 " pdb=" C ASN A 317 " pdb=" N SER A 318 " pdb=" CA SER A 318 " ideal model delta harmonic sigma weight residual 180.00 -154.99 -25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PRO B 345 " pdb=" C PRO B 345 " pdb=" N ASP B 346 " pdb=" CA ASP B 346 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 4546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1184 0.144 - 0.288: 18 0.288 - 0.432: 1 0.432 - 0.576: 0 0.576 - 0.720: 1 Chirality restraints: 1204 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.16 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA ASP A 272 " pdb=" N ASP A 272 " pdb=" C ASP A 272 " pdb=" CB ASP A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1201 not shown) Planarity restraints: 1285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 214 " -0.058 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO A 215 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 454 " -0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO B 455 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 455 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 455 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 454 " -0.013 2.00e-02 2.50e+03 1.87e-02 6.96e+00 pdb=" CG TYR A 454 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 454 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 454 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 454 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 454 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 454 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 454 " 0.002 2.00e-02 2.50e+03 ... (remaining 1282 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2214 2.82 - 3.34: 6433 3.34 - 3.86: 11916 3.86 - 4.38: 13962 4.38 - 4.90: 24177 Nonbonded interactions: 58702 Sorted by model distance: nonbonded pdb=" O SER B 211 " pdb=" OG SER B 211 " model vdw 2.298 3.040 nonbonded pdb=" O LEU A 255 " pdb=" OG SER A 528 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR A 251 " pdb=" OE2 GLU A 472 " model vdw 2.321 3.040 nonbonded pdb=" O SER A 302 " pdb=" OG SER A 302 " model vdw 2.331 3.040 nonbonded pdb=" ND1 HIS B 352 " pdb=" O GLU B 354 " model vdw 2.333 3.120 ... (remaining 58697 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: 1.180 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.360 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 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 : 0.008 0.083 7584 Z= 0.377 Angle : 1.061 12.700 10328 Z= 0.560 Chirality : 0.061 0.720 1204 Planarity : 0.007 0.088 1281 Dihedral : 15.871 102.405 2818 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.49 % Favored : 90.98 % Rotamer: Outliers : 0.51 % Allowed : 5.62 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.22), residues: 931 helix: -1.62 (0.18), residues: 501 sheet: -0.67 (0.63), residues: 66 loop : -2.95 (0.26), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 220 HIS 0.010 0.002 HIS B 466 PHE 0.025 0.003 PHE A 627 TYR 0.045 0.003 TYR A 454 ARG 0.005 0.001 ARG A 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 4) link_NAG-ASN : angle 4.45150 ( 12) link_BETA1-4 : bond 0.01568 ( 4) link_BETA1-4 : angle 4.40590 ( 12) hydrogen bonds : bond 0.17961 ( 393) hydrogen bonds : angle 6.51126 ( 1110) SS BOND : bond 0.00709 ( 1) SS BOND : angle 3.26987 ( 2) covalent geometry : bond 0.00845 ( 7575) covalent geometry : angle 1.04003 (10302) *********************** 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 124 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8346 (mmmm) cc_final: 0.7838 (pttt) REVERT: B 238 SER cc_start: 0.9193 (m) cc_final: 0.8964 (m) REVERT: B 474 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7290 (ttm-80) outliers start: 4 outliers final: 1 residues processed: 122 average time/residue: 1.0545 time to fit residues: 137.1356 Evaluate side-chains 67 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 474 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 258 ASN B 278 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.200257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.100196 restraints weight = 9586.432| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.15 r_work: 0.2961 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7584 Z= 0.140 Angle : 0.721 10.192 10328 Z= 0.354 Chirality : 0.044 0.367 1204 Planarity : 0.005 0.053 1281 Dihedral : 11.304 82.636 1179 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.41 % Favored : 92.48 % Rotamer: Outliers : 2.30 % Allowed : 11.11 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 931 helix: 0.34 (0.22), residues: 506 sheet: -0.52 (0.66), residues: 64 loop : -2.21 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 434 HIS 0.011 0.001 HIS A 557 PHE 0.014 0.001 PHE B 187 TYR 0.025 0.002 TYR A 554 ARG 0.005 0.001 ARG B 601 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 4) link_NAG-ASN : angle 3.24063 ( 12) link_BETA1-4 : bond 0.00727 ( 4) link_BETA1-4 : angle 2.17510 ( 12) hydrogen bonds : bond 0.05398 ( 393) hydrogen bonds : angle 4.60164 ( 1110) SS BOND : bond 0.00333 ( 1) SS BOND : angle 1.64374 ( 2) covalent geometry : bond 0.00296 ( 7575) covalent geometry : angle 0.70942 (10302) *********************** 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 98 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 HIS cc_start: 0.6552 (m170) cc_final: 0.6308 (m170) REVERT: A 270 LYS cc_start: 0.6882 (tppt) cc_final: 0.6647 (tppp) REVERT: A 401 LEU cc_start: 0.8480 (pt) cc_final: 0.8104 (mp) REVERT: A 422 GLN cc_start: 0.9041 (mt0) cc_final: 0.8566 (pp30) REVERT: A 423 TYR cc_start: 0.8921 (t80) cc_final: 0.8495 (t80) REVERT: A 516 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7970 (t0) REVERT: A 529 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8044 (OUTLIER) REVERT: B 178 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8071 (pttt) REVERT: B 414 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8964 (pt) REVERT: B 474 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7836 (ttm-80) outliers start: 18 outliers final: 5 residues processed: 96 average time/residue: 0.9740 time to fit residues: 100.5420 Evaluate side-chains 70 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 474 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS ** A 483 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 = 0.4330 r_free = 0.4330 target = 0.196983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.096266 restraints weight = 9754.838| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.07 r_work: 0.2879 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7584 Z= 0.181 Angle : 0.719 7.803 10328 Z= 0.352 Chirality : 0.045 0.336 1204 Planarity : 0.005 0.059 1281 Dihedral : 9.601 69.512 1178 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.16 % Favored : 91.73 % Rotamer: Outliers : 2.81 % Allowed : 13.41 % Favored : 83.78 % 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: -0.16 (0.28), residues: 931 helix: 1.06 (0.23), residues: 510 sheet: -0.07 (0.66), residues: 64 loop : -1.88 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 220 HIS 0.006 0.002 HIS A 557 PHE 0.017 0.002 PHE B 187 TYR 0.032 0.002 TYR B 90 ARG 0.005 0.001 ARG B 601 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 4) link_NAG-ASN : angle 2.80267 ( 12) link_BETA1-4 : bond 0.00896 ( 4) link_BETA1-4 : angle 2.40252 ( 12) hydrogen bonds : bond 0.06235 ( 393) hydrogen bonds : angle 4.39848 ( 1110) SS BOND : bond 0.01030 ( 1) SS BOND : angle 2.87373 ( 2) covalent geometry : bond 0.00427 ( 7575) covalent geometry : angle 0.70779 (10302) *********************** 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 89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 GLN cc_start: 0.9072 (mt0) cc_final: 0.8603 (pp30) REVERT: A 423 TYR cc_start: 0.8965 (t80) cc_final: 0.8587 (OUTLIER) REVERT: A 516 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7956 (t70) REVERT: A 590 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7418 (mm) REVERT: A 597 LEU cc_start: 0.7674 (mm) cc_final: 0.7314 (mt) REVERT: B 178 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8178 (pttt) REVERT: B 414 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8941 (pt) REVERT: B 474 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7783 (mtm-85) outliers start: 22 outliers final: 8 residues processed: 84 average time/residue: 0.8464 time to fit residues: 77.3913 Evaluate side-chains 69 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 474 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 221 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.200031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099501 restraints weight = 9744.799| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.19 r_work: 0.2949 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7584 Z= 0.121 Angle : 0.656 8.500 10328 Z= 0.313 Chirality : 0.042 0.321 1204 Planarity : 0.004 0.049 1281 Dihedral : 8.461 55.943 1178 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.63 % Favored : 92.27 % Rotamer: Outliers : 2.30 % Allowed : 14.81 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.28), residues: 931 helix: 1.48 (0.24), residues: 519 sheet: -0.03 (0.64), residues: 64 loop : -1.72 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 434 HIS 0.006 0.001 HIS B 466 PHE 0.013 0.001 PHE A 234 TYR 0.028 0.001 TYR A 554 ARG 0.004 0.000 ARG B 601 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 4) link_NAG-ASN : angle 2.69081 ( 12) link_BETA1-4 : bond 0.00926 ( 4) link_BETA1-4 : angle 2.33429 ( 12) hydrogen bonds : bond 0.04636 ( 393) hydrogen bonds : angle 4.13639 ( 1110) SS BOND : bond 0.00550 ( 1) SS BOND : angle 2.50752 ( 2) covalent geometry : bond 0.00256 ( 7575) covalent geometry : angle 0.64433 (10302) *********************** 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 86 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8182 (ptp) REVERT: A 219 TRP cc_start: 0.7526 (p-90) cc_final: 0.7050 (p-90) REVERT: A 422 GLN cc_start: 0.9062 (mt0) cc_final: 0.8583 (pp30) REVERT: A 423 TYR cc_start: 0.8900 (t80) cc_final: 0.8619 (OUTLIER) REVERT: A 516 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8028 (t70) REVERT: A 590 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7517 (mm) REVERT: B 178 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8044 (pttt) REVERT: B 414 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9053 (pt) REVERT: B 474 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7736 (mtm-85) outliers start: 18 outliers final: 8 residues processed: 82 average time/residue: 0.9193 time to fit residues: 81.2336 Evaluate side-chains 66 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.198800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099170 restraints weight = 9640.418| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.06 r_work: 0.2920 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7584 Z= 0.128 Angle : 0.647 8.250 10328 Z= 0.311 Chirality : 0.043 0.321 1204 Planarity : 0.004 0.049 1281 Dihedral : 7.561 56.433 1174 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.59 % Favored : 91.30 % Rotamer: Outliers : 2.43 % Allowed : 15.07 % Favored : 82.50 % 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: 0.57 (0.28), residues: 931 helix: 1.64 (0.24), residues: 519 sheet: -0.00 (0.63), residues: 64 loop : -1.54 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 434 HIS 0.005 0.001 HIS B 466 PHE 0.013 0.001 PHE B 187 TYR 0.027 0.001 TYR A 554 ARG 0.008 0.000 ARG A 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 4) link_NAG-ASN : angle 2.52221 ( 12) link_BETA1-4 : bond 0.00892 ( 4) link_BETA1-4 : angle 2.42453 ( 12) hydrogen bonds : bond 0.04765 ( 393) hydrogen bonds : angle 4.09450 ( 1110) SS BOND : bond 0.01382 ( 1) SS BOND : angle 2.38902 ( 2) covalent geometry : bond 0.00283 ( 7575) covalent geometry : angle 0.63571 (10302) *********************** 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 78 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7409 (tp) REVERT: A 516 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8057 (t70) REVERT: A 590 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7563 (mm) REVERT: B 178 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8067 (pttt) REVERT: B 414 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8891 (pt) REVERT: B 474 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7918 (ttm-80) outliers start: 19 outliers final: 8 residues processed: 72 average time/residue: 0.8862 time to fit residues: 69.3310 Evaluate side-chains 69 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 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 = 0.4327 r_free = 0.4327 target = 0.196457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093797 restraints weight = 9773.932| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.21 r_work: 0.2893 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7584 Z= 0.164 Angle : 0.671 9.080 10328 Z= 0.328 Chirality : 0.044 0.312 1204 Planarity : 0.004 0.053 1281 Dihedral : 6.784 55.494 1174 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.06 % Favored : 91.84 % Rotamer: Outliers : 3.19 % Allowed : 14.18 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.28), residues: 931 helix: 1.63 (0.23), residues: 520 sheet: -0.07 (0.61), residues: 64 loop : -1.44 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 492 HIS 0.005 0.001 HIS B 466 PHE 0.015 0.001 PHE B 187 TYR 0.024 0.002 TYR A 554 ARG 0.006 0.001 ARG A 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 4) link_NAG-ASN : angle 2.38845 ( 12) link_BETA1-4 : bond 0.00814 ( 4) link_BETA1-4 : angle 2.57538 ( 12) hydrogen bonds : bond 0.05622 ( 393) hydrogen bonds : angle 4.16250 ( 1110) SS BOND : bond 0.00865 ( 1) SS BOND : angle 2.83339 ( 2) covalent geometry : bond 0.00388 ( 7575) covalent geometry : angle 0.65965 (10302) *********************** 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 85 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7500 (tm) REVERT: A 422 GLN cc_start: 0.9076 (mt0) cc_final: 0.8608 (pp30) REVERT: A 423 TYR cc_start: 0.8939 (t80) cc_final: 0.8452 (OUTLIER) REVERT: A 516 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8068 (t70) REVERT: A 590 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7670 (mm) REVERT: B 178 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8192 (pttt) REVERT: B 414 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8975 (pt) REVERT: B 474 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.7794 (mtm-85) outliers start: 25 outliers final: 11 residues processed: 80 average time/residue: 0.9035 time to fit residues: 78.2012 Evaluate side-chains 69 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 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 = 0.4350 r_free = 0.4350 target = 0.198568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099057 restraints weight = 9689.343| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.10 r_work: 0.2946 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7584 Z= 0.122 Angle : 0.650 8.063 10328 Z= 0.314 Chirality : 0.042 0.312 1204 Planarity : 0.004 0.047 1281 Dihedral : 6.331 51.024 1174 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 2.17 % Allowed : 15.71 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.29), residues: 931 helix: 1.83 (0.23), residues: 522 sheet: -0.06 (0.62), residues: 64 loop : -1.31 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 492 HIS 0.005 0.001 HIS B 466 PHE 0.018 0.001 PHE A 234 TYR 0.012 0.001 TYR A 454 ARG 0.006 0.000 ARG A 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 4) link_NAG-ASN : angle 2.50783 ( 12) link_BETA1-4 : bond 0.00835 ( 4) link_BETA1-4 : angle 2.31190 ( 12) hydrogen bonds : bond 0.04617 ( 393) hydrogen bonds : angle 4.05000 ( 1110) SS BOND : bond 0.00313 ( 1) SS BOND : angle 2.74862 ( 2) covalent geometry : bond 0.00267 ( 7575) covalent geometry : angle 0.63916 (10302) *********************** 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 78 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 400 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7563 (tm) REVERT: A 422 GLN cc_start: 0.9031 (mt0) cc_final: 0.8533 (pp30) REVERT: A 423 TYR cc_start: 0.8892 (t80) cc_final: 0.8416 (t80) REVERT: A 590 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7749 (mt) REVERT: B 50 MET cc_start: 0.9224 (mtp) cc_final: 0.8965 (mtp) REVERT: B 178 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8082 (pttt) REVERT: B 414 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8835 (pt) REVERT: B 474 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7757 (mtm-85) outliers start: 17 outliers final: 9 residues processed: 73 average time/residue: 0.8876 time to fit residues: 70.2880 Evaluate side-chains 66 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 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 = 0.4332 r_free = 0.4332 target = 0.196537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097185 restraints weight = 9862.261| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.05 r_work: 0.2921 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7584 Z= 0.133 Angle : 0.652 9.120 10328 Z= 0.317 Chirality : 0.042 0.313 1204 Planarity : 0.004 0.048 1281 Dihedral : 5.896 45.097 1174 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.41 % Favored : 92.48 % Rotamer: Outliers : 2.17 % Allowed : 15.58 % Favored : 82.25 % 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: 0.92 (0.29), residues: 931 helix: 1.86 (0.23), residues: 522 sheet: -0.08 (0.64), residues: 65 loop : -1.25 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 492 HIS 0.007 0.001 HIS A 557 PHE 0.024 0.001 PHE A 467 TYR 0.023 0.001 TYR A 554 ARG 0.007 0.000 ARG A 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 4) link_NAG-ASN : angle 2.55834 ( 12) link_BETA1-4 : bond 0.00782 ( 4) link_BETA1-4 : angle 2.26021 ( 12) hydrogen bonds : bond 0.04877 ( 393) hydrogen bonds : angle 4.02230 ( 1110) SS BOND : bond 0.00697 ( 1) SS BOND : angle 2.73423 ( 2) covalent geometry : bond 0.00302 ( 7575) covalent geometry : angle 0.64128 (10302) *********************** 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 74 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 219 TRP cc_start: 0.7378 (p-90) cc_final: 0.7153 (p-90) REVERT: A 400 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7612 (tp) REVERT: A 422 GLN cc_start: 0.8963 (mt0) cc_final: 0.8499 (pp30) REVERT: A 423 TYR cc_start: 0.8879 (t80) cc_final: 0.8467 (t80) REVERT: A 490 MET cc_start: 0.6724 (ppp) cc_final: 0.6330 (ppp) REVERT: A 590 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7922 (mt) REVERT: B 178 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8123 (pttt) REVERT: B 414 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8831 (pt) REVERT: B 474 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7740 (mtm-85) outliers start: 17 outliers final: 10 residues processed: 71 average time/residue: 0.9178 time to fit residues: 70.9010 Evaluate side-chains 69 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 16 optimal weight: 0.0030 chunk 87 optimal weight: 0.8980 chunk 38 optimal weight: 0.0030 chunk 77 optimal weight: 0.6980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.199893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101729 restraints weight = 9849.778| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.15 r_work: 0.2992 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7584 Z= 0.111 Angle : 0.627 8.004 10328 Z= 0.302 Chirality : 0.041 0.317 1204 Planarity : 0.004 0.043 1281 Dihedral : 5.477 39.221 1174 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.87 % Favored : 93.02 % Rotamer: Outliers : 1.92 % Allowed : 16.09 % Favored : 81.99 % 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: 1.08 (0.29), residues: 931 helix: 2.02 (0.24), residues: 522 sheet: 0.01 (0.65), residues: 65 loop : -1.25 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 434 HIS 0.006 0.001 HIS A 557 PHE 0.015 0.001 PHE A 467 TYR 0.010 0.001 TYR B 90 ARG 0.006 0.000 ARG A 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 4) link_NAG-ASN : angle 2.67946 ( 12) link_BETA1-4 : bond 0.00781 ( 4) link_BETA1-4 : angle 2.07320 ( 12) hydrogen bonds : bond 0.03982 ( 393) hydrogen bonds : angle 3.90453 ( 1110) SS BOND : bond 0.00192 ( 1) SS BOND : angle 2.87874 ( 2) covalent geometry : bond 0.00238 ( 7575) covalent geometry : angle 0.61560 (10302) *********************** 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 78 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 219 TRP cc_start: 0.7438 (p-90) cc_final: 0.7107 (p-90) REVERT: A 400 LEU cc_start: 0.8009 (mm) cc_final: 0.7595 (tp) REVERT: A 422 GLN cc_start: 0.8945 (mt0) cc_final: 0.8553 (pp30) REVERT: A 423 TYR cc_start: 0.8871 (t80) cc_final: 0.8510 (t80) REVERT: A 590 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8007 (mm) REVERT: B 50 MET cc_start: 0.9203 (mtp) cc_final: 0.8991 (mtp) REVERT: B 178 LYS cc_start: 0.8693 (mmmm) cc_final: 0.7918 (pttt) REVERT: B 414 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8765 (pt) REVERT: B 474 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7645 (mtm-85) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 0.8866 time to fit residues: 71.3544 Evaluate side-chains 68 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.195339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095254 restraints weight = 9795.215| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.06 r_work: 0.2889 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7584 Z= 0.160 Angle : 0.680 10.552 10328 Z= 0.332 Chirality : 0.043 0.314 1204 Planarity : 0.004 0.049 1281 Dihedral : 5.377 35.971 1174 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 1.40 % Allowed : 16.60 % Favored : 81.99 % 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: 0.94 (0.29), residues: 931 helix: 1.85 (0.23), residues: 521 sheet: -0.03 (0.64), residues: 65 loop : -1.19 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 492 HIS 0.006 0.001 HIS A 557 PHE 0.020 0.001 PHE A 467 TYR 0.023 0.002 TYR A 554 ARG 0.005 0.000 ARG A 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 4) link_NAG-ASN : angle 2.66162 ( 12) link_BETA1-4 : bond 0.00705 ( 4) link_BETA1-4 : angle 2.13139 ( 12) hydrogen bonds : bond 0.05489 ( 393) hydrogen bonds : angle 4.05114 ( 1110) SS BOND : bond 0.00855 ( 1) SS BOND : angle 3.18285 ( 2) covalent geometry : bond 0.00378 ( 7575) covalent geometry : angle 0.66895 (10302) ********************** 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 66 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 TRP cc_start: 0.7474 (p-90) cc_final: 0.7095 (p-90) REVERT: A 270 LYS cc_start: 0.7311 (mmmt) cc_final: 0.6863 (tppt) REVERT: A 400 LEU cc_start: 0.8019 (mm) cc_final: 0.7591 (tp) REVERT: A 590 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8097 (mt) REVERT: B 178 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8081 (pttt) REVERT: B 414 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8885 (pt) REVERT: B 474 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7692 (mtm-85) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.9818 time to fit residues: 66.7783 Evaluate side-chains 64 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.195012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097040 restraints weight = 9790.115| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.05 r_work: 0.2920 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7584 Z= 0.128 Angle : 0.651 11.564 10328 Z= 0.315 Chirality : 0.042 0.318 1204 Planarity : 0.004 0.045 1281 Dihedral : 5.194 32.071 1174 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 1.79 % Allowed : 16.48 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.29), residues: 931 helix: 1.96 (0.24), residues: 522 sheet: 0.03 (0.65), residues: 65 loop : -1.13 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 434 HIS 0.005 0.001 HIS B 466 PHE 0.015 0.001 PHE A 467 TYR 0.010 0.001 TYR B 90 ARG 0.006 0.000 ARG A 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 4) link_NAG-ASN : angle 2.70937 ( 12) link_BETA1-4 : bond 0.00771 ( 4) link_BETA1-4 : angle 1.95538 ( 12) hydrogen bonds : bond 0.04661 ( 393) hydrogen bonds : angle 3.96458 ( 1110) SS BOND : bond 0.00576 ( 1) SS BOND : angle 3.00530 ( 2) covalent geometry : bond 0.00287 ( 7575) covalent geometry : angle 0.64034 (10302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7772.85 seconds wall clock time: 132 minutes 33.01 seconds (7953.01 seconds total)