Starting phenix.real_space_refine on Wed Sep 17 08:56:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kju_62377/09_2025/9kju_62377_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kju_62377/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kju_62377/09_2025/9kju_62377_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kju_62377/09_2025/9kju_62377_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kju_62377/09_2025/9kju_62377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kju_62377/09_2025/9kju_62377.map" } resolution = 2.7 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: 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.97, per 1000 atoms: 0.27 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: 0.54 Conformation dependent library (CDL) restraints added in 476.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.25 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: 1.22 Time building geometry restraints manager: 0.70 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: 1.600 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.810 Find NCS groups from input model: 0.060 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:9.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 452 TYR 0.045 0.003 TYR A 454 PHE 0.025 0.003 PHE A 627 TRP 0.018 0.003 TRP A 220 HIS 0.010 0.002 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00845 ( 7575) covalent geometry : angle 1.04003 (10302) SS BOND : bond 0.00709 ( 1) SS BOND : angle 3.26987 ( 2) hydrogen bonds : bond 0.17961 ( 393) hydrogen bonds : angle 6.51126 ( 1110) link_BETA1-4 : bond 0.01568 ( 4) link_BETA1-4 : angle 4.40590 ( 12) link_NAG-ASN : bond 0.00767 ( 4) link_NAG-ASN : angle 4.45150 ( 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 124 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.294 Fit side-chains 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: 0.7839 (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: 0.5420 time to fit residues: 70.0693 Evaluate side-chains 66 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 232 GLN A 353 ASN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.199392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099015 restraints weight = 9685.903| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.12 r_work: 0.2944 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7584 Z= 0.156 Angle : 0.735 10.107 10328 Z= 0.363 Chirality : 0.044 0.370 1204 Planarity : 0.005 0.057 1281 Dihedral : 11.332 82.601 1179 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 2.30 % Allowed : 11.24 % Favored : 86.46 % 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 aren not related in a simple way. whole: -1.12 (0.26), residues: 931 helix: 0.22 (0.22), residues: 513 sheet: -0.53 (0.66), residues: 64 loop : -2.22 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 601 TYR 0.025 0.002 TYR A 554 PHE 0.015 0.001 PHE B 187 TRP 0.020 0.002 TRP A 434 HIS 0.012 0.002 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7575) covalent geometry : angle 0.72350 (10302) SS BOND : bond 0.00367 ( 1) SS BOND : angle 1.84250 ( 2) hydrogen bonds : bond 0.05786 ( 393) hydrogen bonds : angle 4.61254 ( 1110) link_BETA1-4 : bond 0.00828 ( 4) link_BETA1-4 : angle 2.18703 ( 12) link_NAG-ASN : bond 0.00174 ( 4) link_NAG-ASN : angle 3.18125 ( 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 95 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.6882 (tppt) cc_final: 0.6646 (tppp) REVERT: A 401 LEU cc_start: 0.8469 (pt) cc_final: 0.8101 (mp) REVERT: A 516 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7973 (t0) REVERT: A 529 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7967 (OUTLIER) REVERT: B 50 MET cc_start: 0.9244 (mtp) cc_final: 0.9016 (mtp) REVERT: B 178 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8118 (pttt) REVERT: B 414 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8993 (pt) REVERT: B 474 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7843 (ttm-80) outliers start: 18 outliers final: 7 residues processed: 92 average time/residue: 0.4576 time to fit residues: 45.0551 Evaluate side-chains 72 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 423 TYR 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 69 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4361 r_free = 0.4361 target = 0.200002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100638 restraints weight = 9665.191| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.07 r_work: 0.2961 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7584 Z= 0.131 Angle : 0.679 7.795 10328 Z= 0.329 Chirality : 0.043 0.343 1204 Planarity : 0.004 0.050 1281 Dihedral : 9.806 72.516 1178 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 2.55 % Allowed : 12.64 % Favored : 84.80 % 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 aren not related in a simple way. whole: -0.16 (0.28), residues: 931 helix: 1.03 (0.23), residues: 517 sheet: -0.06 (0.66), residues: 64 loop : -1.90 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 601 TYR 0.039 0.002 TYR A 423 PHE 0.014 0.001 PHE B 187 TRP 0.019 0.001 TRP A 220 HIS 0.006 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7575) covalent geometry : angle 0.66720 (10302) SS BOND : bond 0.00941 ( 1) SS BOND : angle 1.90347 ( 2) hydrogen bonds : bond 0.04991 ( 393) hydrogen bonds : angle 4.28378 ( 1110) link_BETA1-4 : bond 0.00825 ( 4) link_BETA1-4 : angle 2.28488 ( 12) link_NAG-ASN : bond 0.00301 ( 4) link_NAG-ASN : angle 2.87118 ( 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 88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 HIS cc_start: 0.6564 (m170) cc_final: 0.6164 (m90) REVERT: A 270 LYS cc_start: 0.6756 (tppt) cc_final: 0.6527 (tppp) REVERT: A 401 LEU cc_start: 0.8415 (pt) cc_final: 0.8118 (tp) REVERT: A 457 MET cc_start: 0.8044 (tpp) cc_final: 0.7775 (tpt) REVERT: A 516 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8002 (t70) REVERT: B 178 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8040 (pttt) REVERT: B 414 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8994 (pt) REVERT: B 474 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7894 (ttm-80) outliers start: 20 outliers final: 5 residues processed: 84 average time/residue: 0.4244 time to fit residues: 38.4898 Evaluate side-chains 69 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain B residue 66 SER 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 474 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 20.0000 chunk 81 optimal weight: 0.0470 chunk 67 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 82 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4365 r_free = 0.4365 target = 0.200484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101651 restraints weight = 9853.808| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.14 r_work: 0.2983 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7584 Z= 0.115 Angle : 0.634 8.314 10328 Z= 0.305 Chirality : 0.042 0.319 1204 Planarity : 0.004 0.047 1281 Dihedral : 8.398 56.923 1178 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.16 % Rotamer: Outliers : 2.04 % Allowed : 14.56 % 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 aren not related in a simple way. whole: 0.34 (0.28), residues: 931 helix: 1.54 (0.24), residues: 517 sheet: 0.03 (0.66), residues: 65 loop : -1.82 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 601 TYR 0.028 0.001 TYR A 554 PHE 0.012 0.001 PHE B 187 TRP 0.024 0.001 TRP A 434 HIS 0.005 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7575) covalent geometry : angle 0.62265 (10302) SS BOND : bond 0.00414 ( 1) SS BOND : angle 2.49489 ( 2) hydrogen bonds : bond 0.04375 ( 393) hydrogen bonds : angle 4.05377 ( 1110) link_BETA1-4 : bond 0.00926 ( 4) link_BETA1-4 : angle 2.31419 ( 12) link_NAG-ASN : bond 0.00295 ( 4) link_NAG-ASN : angle 2.66916 ( 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 88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.8481 (pt) cc_final: 0.8203 (tp) REVERT: A 516 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8101 (t70) REVERT: B 50 MET cc_start: 0.9149 (mtp) cc_final: 0.8909 (mtp) REVERT: B 178 LYS cc_start: 0.8726 (mmmm) cc_final: 0.7969 (pttt) REVERT: B 414 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9056 (pt) REVERT: B 474 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7696 (mtm-85) outliers start: 16 outliers final: 6 residues processed: 83 average time/residue: 0.4140 time to fit residues: 37.0352 Evaluate side-chains 65 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 543 HIS 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 414 LEU Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 91 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 232 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 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 = 0.4348 r_free = 0.4348 target = 0.198239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097723 restraints weight = 9791.219| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.16 r_work: 0.2915 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2912 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 : 0.654 9.846 10328 Z= 0.316 Chirality : 0.043 0.322 1204 Planarity : 0.004 0.050 1281 Dihedral : 7.240 55.141 1174 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.06 % Favored : 91.84 % Rotamer: Outliers : 3.32 % Allowed : 14.81 % Favored : 81.86 % 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 aren not related in a simple way. whole: 0.50 (0.29), residues: 931 helix: 1.60 (0.24), residues: 518 sheet: -0.02 (0.65), residues: 65 loop : -1.61 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 601 TYR 0.027 0.002 TYR A 554 PHE 0.015 0.001 PHE B 187 TRP 0.025 0.002 TRP A 220 HIS 0.005 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7575) covalent geometry : angle 0.64246 (10302) SS BOND : bond 0.00732 ( 1) SS BOND : angle 2.64965 ( 2) hydrogen bonds : bond 0.05077 ( 393) hydrogen bonds : angle 4.05674 ( 1110) link_BETA1-4 : bond 0.00869 ( 4) link_BETA1-4 : angle 2.48977 ( 12) link_NAG-ASN : bond 0.00291 ( 4) link_NAG-ASN : angle 2.42170 ( 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 88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 TRP cc_start: 0.7624 (p-90) cc_final: 0.7275 (p-90) REVERT: A 221 HIS cc_start: 0.6697 (m170) cc_final: 0.6329 (m90) REVERT: A 516 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8043 (t70) REVERT: A 590 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7429 (mm) REVERT: B 178 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8057 (pttt) REVERT: B 286 ASP cc_start: 0.8265 (p0) cc_final: 0.7864 (p0) REVERT: B 414 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8812 (pt) REVERT: B 474 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7690 (mtm-85) outliers start: 26 outliers final: 11 residues processed: 83 average time/residue: 0.4479 time to fit residues: 40.0478 Evaluate side-chains 70 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.198422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098798 restraints weight = 9753.391| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.10 r_work: 0.2938 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7584 Z= 0.129 Angle : 0.637 8.934 10328 Z= 0.308 Chirality : 0.042 0.317 1204 Planarity : 0.004 0.048 1281 Dihedral : 6.718 54.160 1174 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 2.81 % Allowed : 15.33 % Favored : 81.86 % 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 aren not related in a simple way. whole: 0.72 (0.29), residues: 931 helix: 1.72 (0.24), residues: 523 sheet: -0.02 (0.63), residues: 65 loop : -1.42 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 304 TYR 0.027 0.001 TYR A 554 PHE 0.016 0.001 PHE A 545 TRP 0.023 0.001 TRP A 434 HIS 0.005 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7575) covalent geometry : angle 0.62533 (10302) SS BOND : bond 0.00654 ( 1) SS BOND : angle 2.69824 ( 2) hydrogen bonds : bond 0.04786 ( 393) hydrogen bonds : angle 4.01898 ( 1110) link_BETA1-4 : bond 0.00723 ( 4) link_BETA1-4 : angle 2.47344 ( 12) link_NAG-ASN : bond 0.00332 ( 4) link_NAG-ASN : angle 2.42295 ( 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 83 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8143 (ptp) REVERT: A 221 HIS cc_start: 0.6631 (m170) cc_final: 0.6277 (m90) REVERT: A 516 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8060 (t70) REVERT: A 554 TYR cc_start: 0.6450 (p90) cc_final: 0.6240 (p90) REVERT: A 590 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7492 (mm) REVERT: A 597 LEU cc_start: 0.7668 (mm) cc_final: 0.7376 (mt) REVERT: B 50 MET cc_start: 0.9226 (mtp) cc_final: 0.8968 (mtp) REVERT: B 178 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8049 (pttt) REVERT: B 216 ASN cc_start: 0.8153 (t0) cc_final: 0.7949 (t0) REVERT: B 414 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8832 (pt) REVERT: B 474 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7693 (mtm-85) outliers start: 22 outliers final: 11 residues processed: 79 average time/residue: 0.4063 time to fit residues: 34.7554 Evaluate side-chains 73 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS 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 Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 232 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4334 r_free = 0.4334 target = 0.196715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095601 restraints weight = 9769.199| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.18 r_work: 0.2893 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7584 Z= 0.160 Angle : 0.665 9.452 10328 Z= 0.323 Chirality : 0.043 0.311 1204 Planarity : 0.004 0.052 1281 Dihedral : 6.219 50.101 1174 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.49 % Favored : 91.41 % Rotamer: Outliers : 2.81 % Allowed : 15.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.29), residues: 931 helix: 1.67 (0.24), residues: 523 sheet: -0.06 (0.63), residues: 65 loop : -1.33 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 304 TYR 0.024 0.002 TYR A 554 PHE 0.015 0.001 PHE B 187 TRP 0.033 0.002 TRP A 492 HIS 0.005 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7575) covalent geometry : angle 0.65433 (10302) SS BOND : bond 0.00824 ( 1) SS BOND : angle 2.86007 ( 2) hydrogen bonds : bond 0.05498 ( 393) hydrogen bonds : angle 4.08419 ( 1110) link_BETA1-4 : bond 0.00824 ( 4) link_BETA1-4 : angle 2.42237 ( 12) link_NAG-ASN : bond 0.00324 ( 4) link_NAG-ASN : angle 2.38345 ( 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 83 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.7421 (t80) cc_final: 0.7161 (t80) REVERT: A 434 TRP cc_start: 0.5711 (m100) cc_final: 0.5322 (m-90) REVERT: A 516 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7932 (t70) REVERT: A 590 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7642 (mt) REVERT: B 178 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8121 (pttt) REVERT: B 216 ASN cc_start: 0.8228 (t0) cc_final: 0.7974 (t0) REVERT: B 414 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8953 (pt) REVERT: B 474 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7763 (mtm-85) outliers start: 22 outliers final: 12 residues processed: 78 average time/residue: 0.4410 time to fit residues: 37.2219 Evaluate side-chains 73 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 422 GLN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4333 r_free = 0.4333 target = 0.196541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097196 restraints weight = 9871.540| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.10 r_work: 0.2898 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7584 Z= 0.139 Angle : 0.655 9.980 10328 Z= 0.319 Chirality : 0.042 0.313 1204 Planarity : 0.005 0.117 1281 Dihedral : 5.934 44.992 1174 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 2.30 % Allowed : 15.84 % Favored : 81.86 % 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 aren not related in a simple way. whole: 0.87 (0.29), residues: 931 helix: 1.81 (0.24), residues: 521 sheet: -0.10 (0.64), residues: 65 loop : -1.25 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 440 TYR 0.026 0.002 TYR A 554 PHE 0.013 0.001 PHE B 187 TRP 0.031 0.001 TRP A 492 HIS 0.009 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7575) covalent geometry : angle 0.64409 (10302) SS BOND : bond 0.00658 ( 1) SS BOND : angle 2.99047 ( 2) hydrogen bonds : bond 0.05060 ( 393) hydrogen bonds : angle 4.03374 ( 1110) link_BETA1-4 : bond 0.00802 ( 4) link_BETA1-4 : angle 2.28179 ( 12) link_NAG-ASN : bond 0.00335 ( 4) link_NAG-ASN : angle 2.43722 ( 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 78 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.7301 (t80) cc_final: 0.7004 (t80) REVERT: A 257 VAL cc_start: 0.8301 (m) cc_final: 0.8095 (p) REVERT: A 270 LYS cc_start: 0.6800 (tppt) cc_final: 0.6585 (tppt) REVERT: A 434 TRP cc_start: 0.5678 (m100) cc_final: 0.5215 (m-90) REVERT: A 516 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7957 (t70) REVERT: A 590 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7761 (mt) REVERT: B 178 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8094 (pttt) REVERT: B 216 ASN cc_start: 0.8216 (t0) cc_final: 0.7942 (t0) REVERT: B 414 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8934 (pt) REVERT: B 474 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7767 (mtm-85) outliers start: 18 outliers final: 12 residues processed: 74 average time/residue: 0.4553 time to fit residues: 36.3383 Evaluate side-chains 71 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 422 GLN 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4336 r_free = 0.4336 target = 0.196994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098617 restraints weight = 9802.433| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.05 r_work: 0.2929 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7584 Z= 0.123 Angle : 0.640 9.789 10328 Z= 0.310 Chirality : 0.042 0.315 1204 Planarity : 0.004 0.070 1281 Dihedral : 5.600 39.815 1174 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.63 % Favored : 92.27 % Rotamer: Outliers : 2.55 % Allowed : 15.58 % Favored : 81.86 % 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 aren not related in a simple way. whole: 0.97 (0.29), residues: 931 helix: 1.91 (0.24), residues: 521 sheet: -0.06 (0.65), residues: 65 loop : -1.24 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 440 TYR 0.011 0.001 TYR B 90 PHE 0.012 0.001 PHE B 187 TRP 0.037 0.001 TRP A 492 HIS 0.007 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7575) covalent geometry : angle 0.62959 (10302) SS BOND : bond 0.00698 ( 1) SS BOND : angle 2.87907 ( 2) hydrogen bonds : bond 0.04662 ( 393) hydrogen bonds : angle 3.98751 ( 1110) link_BETA1-4 : bond 0.00751 ( 4) link_BETA1-4 : angle 2.17120 ( 12) link_NAG-ASN : bond 0.00336 ( 4) link_NAG-ASN : angle 2.49002 ( 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 79 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8124 (ptp) REVERT: A 234 PHE cc_start: 0.7149 (t80) cc_final: 0.6814 (t80) REVERT: A 270 LYS cc_start: 0.6797 (tppt) cc_final: 0.6364 (tppt) REVERT: A 434 TRP cc_start: 0.5630 (m100) cc_final: 0.5190 (m-90) REVERT: A 490 MET cc_start: 0.6561 (ppp) cc_final: 0.6164 (ppp) REVERT: A 590 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7910 (mt) REVERT: B 50 MET cc_start: 0.9218 (mtp) cc_final: 0.8972 (mtp) REVERT: B 178 LYS cc_start: 0.8804 (mmmm) cc_final: 0.8037 (pttt) REVERT: B 216 ASN cc_start: 0.8226 (t0) cc_final: 0.7965 (t0) REVERT: B 414 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8805 (pt) REVERT: B 474 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7672 (mtm-85) outliers start: 20 outliers final: 12 residues processed: 74 average time/residue: 0.4510 time to fit residues: 35.9856 Evaluate side-chains 71 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 422 GLN 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 57 VAL 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 303 GLN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 18 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 9 optimal weight: 0.0070 chunk 47 optimal weight: 0.1980 chunk 27 optimal weight: 30.0000 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 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 = 0.4349 r_free = 0.4349 target = 0.198075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099717 restraints weight = 9789.616| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.11 r_work: 0.2966 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7584 Z= 0.117 Angle : 0.631 8.976 10328 Z= 0.305 Chirality : 0.042 0.318 1204 Planarity : 0.004 0.045 1281 Dihedral : 5.350 35.767 1174 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.63 % Favored : 92.27 % Rotamer: Outliers : 2.30 % Allowed : 15.84 % Favored : 81.86 % 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 aren not related in a simple way. whole: 1.06 (0.29), residues: 931 helix: 2.05 (0.24), residues: 518 sheet: 0.03 (0.65), residues: 65 loop : -1.32 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.020 0.001 TYR A 554 PHE 0.011 0.001 PHE B 187 TRP 0.032 0.001 TRP A 492 HIS 0.006 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7575) covalent geometry : angle 0.62036 (10302) SS BOND : bond 0.00559 ( 1) SS BOND : angle 2.72263 ( 2) hydrogen bonds : bond 0.04347 ( 393) hydrogen bonds : angle 3.92303 ( 1110) link_BETA1-4 : bond 0.00726 ( 4) link_BETA1-4 : angle 2.06295 ( 12) link_NAG-ASN : bond 0.00371 ( 4) link_NAG-ASN : angle 2.54991 ( 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 81 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8128 (ptp) REVERT: A 234 PHE cc_start: 0.7176 (t80) cc_final: 0.6751 (t80) REVERT: A 434 TRP cc_start: 0.5579 (m100) cc_final: 0.5127 (m-90) REVERT: A 490 MET cc_start: 0.6643 (ppp) cc_final: 0.6159 (ppp) REVERT: A 590 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7938 (mt) REVERT: B 50 MET cc_start: 0.9208 (mtp) cc_final: 0.8991 (mtp) REVERT: B 178 LYS cc_start: 0.8706 (mmmm) cc_final: 0.7941 (pttt) REVERT: B 216 ASN cc_start: 0.8217 (t0) cc_final: 0.7956 (t0) REVERT: B 414 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8758 (pt) REVERT: B 474 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7659 (mtm-85) outliers start: 18 outliers final: 10 residues processed: 77 average time/residue: 0.4554 time to fit residues: 37.7811 Evaluate side-chains 72 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 422 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 22 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 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 = 0.4319 r_free = 0.4319 target = 0.194702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096203 restraints weight = 9774.995| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.06 r_work: 0.2900 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7584 Z= 0.139 Angle : 0.661 8.806 10328 Z= 0.320 Chirality : 0.043 0.318 1204 Planarity : 0.005 0.092 1281 Dihedral : 5.236 32.277 1174 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.20 % Favored : 92.70 % Rotamer: Outliers : 1.92 % Allowed : 16.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.29), residues: 931 helix: 1.96 (0.24), residues: 518 sheet: 0.07 (0.65), residues: 65 loop : -1.25 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 440 TYR 0.013 0.001 TYR B 142 PHE 0.014 0.001 PHE B 187 TRP 0.029 0.001 TRP A 492 HIS 0.006 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7575) covalent geometry : angle 0.65129 (10302) SS BOND : bond 0.00729 ( 1) SS BOND : angle 2.83024 ( 2) hydrogen bonds : bond 0.04959 ( 393) hydrogen bonds : angle 3.98830 ( 1110) link_BETA1-4 : bond 0.00731 ( 4) link_BETA1-4 : angle 2.04605 ( 12) link_NAG-ASN : bond 0.00366 ( 4) link_NAG-ASN : angle 2.55413 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3940.74 seconds wall clock time: 67 minutes 41.06 seconds (4061.06 seconds total)