Starting phenix.real_space_refine on Wed Mar 4 00:35:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zay_14582/03_2026/7zay_14582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zay_14582/03_2026/7zay_14582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zay_14582/03_2026/7zay_14582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zay_14582/03_2026/7zay_14582.map" model { file = "/net/cci-nas-00/data/ceres_data/7zay_14582/03_2026/7zay_14582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zay_14582/03_2026/7zay_14582.cif" } resolution = 2.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 46 5.16 5 C 6010 2.51 5 N 1571 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4573 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 4 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4688 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.24, per 1000 atoms: 0.24 Number of scatterers: 9339 At special positions: 0 Unit cell: (97.44, 102.48, 102.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 2 15.00 O 1710 8.00 N 1571 7.00 C 6010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 800 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 470.6 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 37.2% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 94 through 98 removed outlier: 4.026A pdb=" N LYS A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.765A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A 387 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 418 through 433 Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.885A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 447' Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 546 through 551 removed outlier: 3.969A pdb=" N ARG A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 551 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.606A pdb=" N TYR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.550A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 699 through 713 Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.704A pdb=" N ALA B 150 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 removed outlier: 3.548A pdb=" N THR B 164 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.994A pdb=" N LYS B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 4.206A pdb=" N GLN B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 314' Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.971A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.686A pdb=" N ILE B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 400 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 432 through 439 removed outlier: 3.826A pdb=" N GLY B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 518 through 524 removed outlier: 3.581A pdb=" N ASN B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 524 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.589A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.721A pdb=" N TYR B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.853A pdb=" N ALA B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 685 removed outlier: 3.705A pdb=" N CYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.341A pdb=" N TYR A 117 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA A 219 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 194 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 216 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 234 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 218 " --> pdb=" O ILE A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 295 removed outlier: 4.039A pdb=" N LEU A 335 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 267 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 360 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 510 through 514 removed outlier: 6.696A pdb=" N PHE A 480 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 514 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 482 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 624 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 Processing sheet with id=AA5, first strand: chain 'A' and resid 722 through 726 removed outlier: 6.991A pdb=" N VAL B 643 " --> pdb=" O HIS B 694 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA B 696 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS B 645 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 563 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL B 646 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY B 565 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR B 457 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE B 537 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 459 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 512 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP B 489 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 218 removed outlier: 4.680A pdb=" N PHE B 217 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 281 through 283 removed outlier: 6.153A pdb=" N PHE B 253 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 319 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 255 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 316 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 342 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS B 318 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AB2, first strand: chain 'B' and resid 579 through 583 removed outlier: 3.589A pdb=" N LEU B 572 " --> pdb=" O LYS B 581 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 813 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: 1.59 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2958 1.34 - 1.46: 2340 1.46 - 1.58: 4214 1.58 - 1.70: 2 1.70 - 1.82: 71 Bond restraints: 9585 Sorted by residual: bond pdb=" O1A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.80e-02 3.09e+03 6.21e+00 bond pdb=" C1 NAG A 800 " pdb=" O5 NAG A 800 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 9580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 12930 2.89 - 5.77: 87 5.77 - 8.66: 9 8.66 - 11.54: 2 11.54 - 14.43: 1 Bond angle restraints: 13029 Sorted by residual: angle pdb=" C GLY B 260 " pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" O5' UDP A 801 " pdb=" PA UDP A 801 " pdb=" O1A UDP A 801 " ideal model delta sigma weight residual 106.70 111.08 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " pdb=" O3A UDP A 801 " ideal model delta sigma weight residual 105.97 110.23 -4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" N LEU B 261 " pdb=" CA LEU B 261 " pdb=" CB LEU B 261 " ideal model delta sigma weight residual 110.49 117.47 -6.98 1.69e+00 3.50e-01 1.70e+01 angle pdb=" CA LEU B 261 " pdb=" CB LEU B 261 " pdb=" CG LEU B 261 " ideal model delta sigma weight residual 116.30 130.73 -14.43 3.50e+00 8.16e-02 1.70e+01 ... (remaining 13024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 5486 21.82 - 43.64: 256 43.64 - 65.46: 37 65.46 - 87.28: 12 87.28 - 109.10: 6 Dihedral angle restraints: 5797 sinusoidal: 2410 harmonic: 3387 Sorted by residual: dihedral pdb=" CD ARG A 723 " pdb=" NE ARG A 723 " pdb=" CZ ARG A 723 " pdb=" NH1 ARG A 723 " ideal model delta sinusoidal sigma weight residual 0.00 71.37 -71.37 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA ALA B 202 " pdb=" C ALA B 202 " pdb=" N LEU B 203 " pdb=" CA LEU B 203 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.61 109.10 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 5794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1178 0.054 - 0.108: 217 0.108 - 0.161: 34 0.161 - 0.215: 3 0.215 - 0.269: 1 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA PRO B 263 " pdb=" N PRO B 263 " pdb=" C PRO B 263 " pdb=" CB PRO B 263 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE B 344 " pdb=" CA ILE B 344 " pdb=" CG1 ILE B 344 " pdb=" CG2 ILE B 344 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 1430 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 723 " 0.882 9.50e-02 1.11e+02 3.97e-01 1.07e+02 pdb=" NE ARG A 723 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 723 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 723 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 723 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 562 " -0.225 9.50e-02 1.11e+02 1.02e-01 8.22e+00 pdb=" NE ARG B 562 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 562 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG B 562 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 562 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 196 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO B 197 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 197 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 197 " 0.025 5.00e-02 4.00e+02 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 865 2.74 - 3.28: 9521 3.28 - 3.82: 15843 3.82 - 4.36: 19801 4.36 - 4.90: 32647 Nonbonded interactions: 78677 Sorted by model distance: nonbonded pdb=" O ILE B 376 " pdb=" OG SER B 379 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 271 " pdb=" O3B UDP A 801 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 223 " pdb=" NE2 HIS B 88 " model vdw 2.238 3.120 nonbonded pdb=" O PRO B 560 " pdb=" ND1 HIS B 601 " model vdw 2.253 3.120 nonbonded pdb=" OH TYR A 626 " pdb=" NE2 HIS A 631 " model vdw 2.261 3.120 ... (remaining 78672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.260 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.240 Find NCS groups from input model: 0.050 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:7.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.003 0.045 9599 Z= 0.127 Angle : 0.613 14.426 13061 Z= 0.310 Chirality : 0.044 0.269 1433 Planarity : 0.011 0.397 1650 Dihedral : 13.247 109.101 3579 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.82 % Favored : 92.01 % Rotamer: Outliers : 1.09 % Allowed : 7.42 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1126 helix: 0.29 (0.29), residues: 354 sheet: -2.14 (0.49), residues: 105 loop : -1.33 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.001 ARG A 723 TYR 0.009 0.001 TYR A 608 PHE 0.009 0.001 PHE B 400 TRP 0.014 0.001 TRP A 711 HIS 0.010 0.001 HIS B 694 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9585) covalent geometry : angle 0.61072 (13029) SS BOND : bond 0.00288 ( 10) SS BOND : angle 0.79467 ( 20) hydrogen bonds : bond 0.14889 ( 294) hydrogen bonds : angle 7.04437 ( 813) link_BETA1-4 : bond 0.00450 ( 2) link_BETA1-4 : angle 1.34593 ( 6) link_NAG-ASN : bond 0.00196 ( 2) link_NAG-ASN : angle 2.14764 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7245 (m-80) cc_final: 0.7040 (m-80) REVERT: A 420 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 478 SER cc_start: 0.7735 (p) cc_final: 0.7275 (t) REVERT: A 670 ILE cc_start: 0.8002 (mm) cc_final: 0.7766 (mm) REVERT: B 388 MET cc_start: 0.7140 (mtp) cc_final: 0.6859 (mtp) REVERT: B 484 LYS cc_start: 0.4508 (OUTLIER) cc_final: 0.4284 (ttmm) REVERT: B 695 ARG cc_start: 0.7137 (ptt-90) cc_final: 0.6737 (ptt-90) outliers start: 11 outliers final: 1 residues processed: 264 average time/residue: 0.4874 time to fit residues: 137.8752 Evaluate side-chains 195 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 484 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 471 ASN B 162 GLN B 200 ASN B 262 HIS B 389 GLN B 412 GLN B 454 GLN B 550 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.238011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.206627 restraints weight = 11317.407| |-----------------------------------------------------------------------------| r_work (start): 0.4605 rms_B_bonded: 2.66 r_work: 0.4473 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9599 Z= 0.143 Angle : 0.673 11.886 13061 Z= 0.335 Chirality : 0.045 0.225 1433 Planarity : 0.005 0.068 1650 Dihedral : 9.228 89.251 1379 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 2.97 % Allowed : 15.43 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.25), residues: 1126 helix: 0.34 (0.28), residues: 365 sheet: -1.96 (0.50), residues: 101 loop : -1.14 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 595 TYR 0.015 0.001 TYR A 592 PHE 0.014 0.001 PHE B 680 TRP 0.017 0.001 TRP A 711 HIS 0.006 0.001 HIS B 694 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9585) covalent geometry : angle 0.66803 (13029) SS BOND : bond 0.00550 ( 10) SS BOND : angle 1.35116 ( 20) hydrogen bonds : bond 0.04369 ( 294) hydrogen bonds : angle 5.55370 ( 813) link_BETA1-4 : bond 0.00365 ( 2) link_BETA1-4 : angle 2.30584 ( 6) link_NAG-ASN : bond 0.00195 ( 2) link_NAG-ASN : angle 2.12495 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7631 (m-80) cc_final: 0.7307 (m-80) REVERT: A 420 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 478 SER cc_start: 0.7847 (p) cc_final: 0.7327 (t) REVERT: B 388 MET cc_start: 0.7101 (mtp) cc_final: 0.6756 (mtp) REVERT: B 441 SER cc_start: 0.8099 (p) cc_final: 0.7796 (t) REVERT: B 452 GLN cc_start: 0.7082 (mt0) cc_final: 0.6780 (mp10) REVERT: B 592 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7183 (mtm) REVERT: B 624 MET cc_start: 0.7465 (mmm) cc_final: 0.7159 (mmm) REVERT: B 695 ARG cc_start: 0.7532 (ptt-90) cc_final: 0.7311 (ptt-90) outliers start: 30 outliers final: 14 residues processed: 221 average time/residue: 0.4197 time to fit residues: 100.9040 Evaluate side-chains 186 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 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 254 ASN A 287 HIS A 397 HIS A 431 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 313 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.230336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.197678 restraints weight = 11410.883| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 2.72 r_work: 0.4373 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 9599 Z= 0.231 Angle : 0.723 10.247 13061 Z= 0.366 Chirality : 0.049 0.252 1433 Planarity : 0.005 0.055 1650 Dihedral : 8.808 87.665 1375 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 3.96 % Allowed : 17.11 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.25), residues: 1126 helix: -0.04 (0.27), residues: 368 sheet: -1.64 (0.54), residues: 89 loop : -1.17 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 394 TYR 0.023 0.002 TYR B 107 PHE 0.021 0.002 PHE B 604 TRP 0.022 0.002 TRP A 711 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 9585) covalent geometry : angle 0.71790 (13029) SS BOND : bond 0.00820 ( 10) SS BOND : angle 1.40142 ( 20) hydrogen bonds : bond 0.04969 ( 294) hydrogen bonds : angle 5.57902 ( 813) link_BETA1-4 : bond 0.00255 ( 2) link_BETA1-4 : angle 2.77873 ( 6) link_NAG-ASN : bond 0.00105 ( 2) link_NAG-ASN : angle 2.33475 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7774 (m-80) cc_final: 0.7436 (m-80) REVERT: A 420 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7486 (tm-30) REVERT: A 478 SER cc_start: 0.7919 (p) cc_final: 0.7418 (t) REVERT: B 388 MET cc_start: 0.7128 (mtp) cc_final: 0.6846 (mtp) REVERT: B 441 SER cc_start: 0.8186 (p) cc_final: 0.7863 (t) REVERT: B 452 GLN cc_start: 0.7246 (mt0) cc_final: 0.6967 (mp10) REVERT: B 561 ASP cc_start: 0.7280 (p0) cc_final: 0.6848 (t0) REVERT: B 624 MET cc_start: 0.7569 (mmm) cc_final: 0.7308 (mmm) outliers start: 40 outliers final: 18 residues processed: 213 average time/residue: 0.4355 time to fit residues: 100.5471 Evaluate side-chains 185 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 chunk 104 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 72 optimal weight: 0.0070 chunk 89 optimal weight: 0.0270 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** 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 = 0.4920 r_free = 0.4920 target = 0.237540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.205840 restraints weight = 11420.152| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 2.66 r_work: 0.4472 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9599 Z= 0.125 Angle : 0.655 10.709 13061 Z= 0.323 Chirality : 0.045 0.330 1433 Planarity : 0.004 0.045 1650 Dihedral : 8.127 84.915 1375 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.39 % Favored : 93.34 % Rotamer: Outliers : 2.97 % Allowed : 18.79 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.25), residues: 1126 helix: 0.29 (0.27), residues: 366 sheet: -1.81 (0.51), residues: 109 loop : -1.01 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 394 TYR 0.015 0.001 TYR A 592 PHE 0.029 0.001 PHE A 577 TRP 0.021 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9585) covalent geometry : angle 0.65150 (13029) SS BOND : bond 0.00318 ( 10) SS BOND : angle 1.11868 ( 20) hydrogen bonds : bond 0.03738 ( 294) hydrogen bonds : angle 5.19169 ( 813) link_BETA1-4 : bond 0.00444 ( 2) link_BETA1-4 : angle 2.22739 ( 6) link_NAG-ASN : bond 0.00251 ( 2) link_NAG-ASN : angle 2.08547 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7642 (m-80) cc_final: 0.7329 (m-80) REVERT: A 420 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 478 SER cc_start: 0.7814 (p) cc_final: 0.7296 (t) REVERT: B 388 MET cc_start: 0.7125 (mtp) cc_final: 0.6483 (ptp) REVERT: B 441 SER cc_start: 0.8082 (p) cc_final: 0.7792 (t) REVERT: B 561 ASP cc_start: 0.7073 (p0) cc_final: 0.6742 (t0) REVERT: B 592 MET cc_start: 0.7627 (mtp) cc_final: 0.7319 (mtm) outliers start: 30 outliers final: 19 residues processed: 202 average time/residue: 0.4184 time to fit residues: 91.9636 Evaluate side-chains 183 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 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 254 ASN A 431 GLN B 161 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.234792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.202846 restraints weight = 11376.650| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 2.71 r_work: 0.4439 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9599 Z= 0.146 Angle : 0.652 9.802 13061 Z= 0.323 Chirality : 0.046 0.280 1433 Planarity : 0.004 0.044 1650 Dihedral : 8.052 83.404 1375 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.57 % Favored : 93.16 % Rotamer: Outliers : 3.36 % Allowed : 19.29 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.25), residues: 1126 helix: 0.24 (0.27), residues: 375 sheet: -1.84 (0.50), residues: 114 loop : -0.93 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 394 TYR 0.026 0.002 TYR B 107 PHE 0.020 0.001 PHE A 577 TRP 0.022 0.002 TRP A 711 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9585) covalent geometry : angle 0.64758 (13029) SS BOND : bond 0.00457 ( 10) SS BOND : angle 1.19812 ( 20) hydrogen bonds : bond 0.04008 ( 294) hydrogen bonds : angle 5.14589 ( 813) link_BETA1-4 : bond 0.00467 ( 2) link_BETA1-4 : angle 2.55672 ( 6) link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 2.19647 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7671 (m-80) cc_final: 0.7318 (m-80) REVERT: A 420 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7373 (tm-30) REVERT: A 478 SER cc_start: 0.7835 (p) cc_final: 0.7319 (t) REVERT: B 80 ARG cc_start: 0.7202 (ttm110) cc_final: 0.6616 (ptm160) REVERT: B 192 LEU cc_start: 0.8116 (mt) cc_final: 0.7889 (mt) REVERT: B 314 GLU cc_start: 0.7847 (mp0) cc_final: 0.6728 (mp0) REVERT: B 388 MET cc_start: 0.7145 (mtp) cc_final: 0.6795 (mtp) REVERT: B 441 SER cc_start: 0.8127 (p) cc_final: 0.7836 (t) REVERT: B 452 GLN cc_start: 0.7064 (mt0) cc_final: 0.6852 (mp10) REVERT: B 561 ASP cc_start: 0.7103 (p0) cc_final: 0.6751 (t0) REVERT: B 592 MET cc_start: 0.7695 (mtp) cc_final: 0.7391 (mtm) REVERT: B 624 MET cc_start: 0.7539 (mmm) cc_final: 0.7236 (mmm) outliers start: 34 outliers final: 17 residues processed: 202 average time/residue: 0.4390 time to fit residues: 96.1318 Evaluate side-chains 183 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.230149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.197759 restraints weight = 11443.677| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 2.69 r_work: 0.4381 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9599 Z= 0.218 Angle : 0.722 12.194 13061 Z= 0.359 Chirality : 0.048 0.362 1433 Planarity : 0.005 0.041 1650 Dihedral : 8.313 85.470 1375 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.93 % Favored : 92.81 % Rotamer: Outliers : 4.25 % Allowed : 18.69 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.25), residues: 1126 helix: -0.10 (0.26), residues: 381 sheet: -1.68 (0.54), residues: 102 loop : -1.08 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 394 TYR 0.024 0.002 TYR A 467 PHE 0.023 0.002 PHE A 577 TRP 0.024 0.002 TRP A 200 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9585) covalent geometry : angle 0.71701 (13029) SS BOND : bond 0.00535 ( 10) SS BOND : angle 1.29065 ( 20) hydrogen bonds : bond 0.04652 ( 294) hydrogen bonds : angle 5.33210 ( 813) link_BETA1-4 : bond 0.00402 ( 2) link_BETA1-4 : angle 2.86366 ( 6) link_NAG-ASN : bond 0.00195 ( 2) link_NAG-ASN : angle 2.33748 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7727 (m-80) cc_final: 0.7418 (m-80) REVERT: A 420 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 478 SER cc_start: 0.7928 (p) cc_final: 0.7433 (t) REVERT: B 80 ARG cc_start: 0.7229 (ttm110) cc_final: 0.6873 (tpp-160) REVERT: B 192 LEU cc_start: 0.8179 (mt) cc_final: 0.7959 (mt) REVERT: B 310 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 388 MET cc_start: 0.7112 (mtp) cc_final: 0.6776 (mtp) REVERT: B 624 MET cc_start: 0.7559 (mmm) cc_final: 0.7306 (mmm) outliers start: 43 outliers final: 27 residues processed: 202 average time/residue: 0.4566 time to fit residues: 99.7909 Evaluate side-chains 191 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 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 254 ASN A 431 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.233917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.201941 restraints weight = 11436.989| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 2.70 r_work: 0.4428 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9599 Z= 0.144 Angle : 0.702 10.980 13061 Z= 0.344 Chirality : 0.046 0.356 1433 Planarity : 0.004 0.042 1650 Dihedral : 8.082 82.811 1375 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.95 % Favored : 93.78 % Rotamer: Outliers : 3.66 % Allowed : 20.38 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.25), residues: 1126 helix: 0.11 (0.27), residues: 376 sheet: -1.84 (0.50), residues: 114 loop : -0.92 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.022 0.001 TYR A 467 PHE 0.033 0.002 PHE A 577 TRP 0.027 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9585) covalent geometry : angle 0.69777 (13029) SS BOND : bond 0.00336 ( 10) SS BOND : angle 1.31825 ( 20) hydrogen bonds : bond 0.04015 ( 294) hydrogen bonds : angle 5.14785 ( 813) link_BETA1-4 : bond 0.00481 ( 2) link_BETA1-4 : angle 2.47954 ( 6) link_NAG-ASN : bond 0.00226 ( 2) link_NAG-ASN : angle 2.16402 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7682 (m-80) cc_final: 0.7396 (m-80) REVERT: A 420 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 478 SER cc_start: 0.7878 (p) cc_final: 0.7367 (t) REVERT: A 577 PHE cc_start: 0.6885 (t80) cc_final: 0.6629 (t80) REVERT: B 80 ARG cc_start: 0.7164 (ttm110) cc_final: 0.6797 (tpp-160) REVERT: B 209 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5282 (mtp85) REVERT: B 276 HIS cc_start: 0.4684 (OUTLIER) cc_final: 0.4077 (p90) REVERT: B 310 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 388 MET cc_start: 0.7151 (mtp) cc_final: 0.6800 (mtp) REVERT: B 441 SER cc_start: 0.8126 (p) cc_final: 0.7821 (t) REVERT: B 624 MET cc_start: 0.7575 (mmm) cc_final: 0.7338 (mmm) outliers start: 37 outliers final: 21 residues processed: 204 average time/residue: 0.4329 time to fit residues: 96.1131 Evaluate side-chains 185 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN A 721 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.235208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.203296 restraints weight = 11375.341| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 2.69 r_work: 0.4442 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9599 Z= 0.139 Angle : 0.696 11.752 13061 Z= 0.340 Chirality : 0.046 0.321 1433 Planarity : 0.004 0.042 1650 Dihedral : 7.933 79.645 1375 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.22 % Favored : 93.52 % Rotamer: Outliers : 3.76 % Allowed : 20.67 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1126 helix: 0.24 (0.27), residues: 373 sheet: -1.78 (0.50), residues: 114 loop : -0.87 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.028 0.001 TYR A 467 PHE 0.027 0.002 PHE A 577 TRP 0.030 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9585) covalent geometry : angle 0.69203 (13029) SS BOND : bond 0.00382 ( 10) SS BOND : angle 1.27949 ( 20) hydrogen bonds : bond 0.03941 ( 294) hydrogen bonds : angle 5.07269 ( 813) link_BETA1-4 : bond 0.00448 ( 2) link_BETA1-4 : angle 2.45384 ( 6) link_NAG-ASN : bond 0.00192 ( 2) link_NAG-ASN : angle 2.14301 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7636 (m-80) cc_final: 0.7267 (m-80) REVERT: A 420 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 478 SER cc_start: 0.7893 (p) cc_final: 0.7355 (t) REVERT: A 577 PHE cc_start: 0.6890 (t80) cc_final: 0.6658 (t80) REVERT: B 80 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6605 (ptm160) REVERT: B 209 ARG cc_start: 0.5892 (OUTLIER) cc_final: 0.5350 (mtp85) REVERT: B 276 HIS cc_start: 0.4655 (OUTLIER) cc_final: 0.4059 (p90) REVERT: B 310 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 388 MET cc_start: 0.7127 (mtp) cc_final: 0.6777 (mtp) REVERT: B 436 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7851 (mtmm) REVERT: B 441 SER cc_start: 0.8110 (p) cc_final: 0.7808 (t) REVERT: B 561 ASP cc_start: 0.7140 (p0) cc_final: 0.6758 (t0) REVERT: B 624 MET cc_start: 0.7624 (mmm) cc_final: 0.7376 (mmm) outliers start: 38 outliers final: 21 residues processed: 205 average time/residue: 0.4275 time to fit residues: 95.3105 Evaluate side-chains 192 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 0.9980 chunk 65 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 107 optimal weight: 0.0670 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN A 721 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.237350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.205666 restraints weight = 11369.148| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 2.70 r_work: 0.4471 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9599 Z= 0.129 Angle : 0.694 10.611 13061 Z= 0.339 Chirality : 0.046 0.329 1433 Planarity : 0.004 0.042 1650 Dihedral : 7.704 74.866 1375 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.95 % Favored : 93.69 % Rotamer: Outliers : 2.87 % Allowed : 21.36 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.25), residues: 1126 helix: 0.35 (0.27), residues: 374 sheet: -1.73 (0.50), residues: 114 loop : -0.79 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 595 TYR 0.031 0.001 TYR B 107 PHE 0.031 0.001 PHE B 400 TRP 0.031 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9585) covalent geometry : angle 0.68984 (13029) SS BOND : bond 0.00273 ( 10) SS BOND : angle 1.04762 ( 20) hydrogen bonds : bond 0.03720 ( 294) hydrogen bonds : angle 4.97312 ( 813) link_BETA1-4 : bond 0.00441 ( 2) link_BETA1-4 : angle 2.36810 ( 6) link_NAG-ASN : bond 0.00222 ( 2) link_NAG-ASN : angle 2.10846 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7613 (m-80) cc_final: 0.7278 (m-80) REVERT: A 263 MET cc_start: 0.7048 (ttm) cc_final: 0.6802 (ttm) REVERT: A 420 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 478 SER cc_start: 0.7914 (p) cc_final: 0.7363 (t) REVERT: B 80 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6593 (ptm160) REVERT: B 87 MET cc_start: 0.6357 (mmm) cc_final: 0.5538 (mmm) REVERT: B 276 HIS cc_start: 0.4657 (OUTLIER) cc_final: 0.4018 (p90) REVERT: B 310 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 388 MET cc_start: 0.7100 (mtp) cc_final: 0.6500 (ptp) REVERT: B 436 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7815 (mtmm) REVERT: B 441 SER cc_start: 0.8088 (p) cc_final: 0.7809 (t) REVERT: B 561 ASP cc_start: 0.7097 (p0) cc_final: 0.6762 (t0) REVERT: B 624 MET cc_start: 0.7570 (mmm) cc_final: 0.7336 (mmm) outliers start: 29 outliers final: 17 residues processed: 192 average time/residue: 0.4301 time to fit residues: 89.6980 Evaluate side-chains 184 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 88 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN A 721 GLN B 176 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 389 GLN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.235662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.203690 restraints weight = 11344.273| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 2.70 r_work: 0.4447 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9599 Z= 0.148 Angle : 0.710 10.600 13061 Z= 0.348 Chirality : 0.046 0.325 1433 Planarity : 0.004 0.047 1650 Dihedral : 7.651 72.312 1375 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.13 % Favored : 93.61 % Rotamer: Outliers : 2.47 % Allowed : 22.16 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.25), residues: 1126 helix: 0.36 (0.27), residues: 374 sheet: -1.74 (0.50), residues: 114 loop : -0.77 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 595 TYR 0.036 0.002 TYR A 467 PHE 0.025 0.002 PHE B 400 TRP 0.034 0.002 TRP A 200 HIS 0.007 0.001 HIS B 262 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9585) covalent geometry : angle 0.70613 (13029) SS BOND : bond 0.00323 ( 10) SS BOND : angle 1.11307 ( 20) hydrogen bonds : bond 0.03925 ( 294) hydrogen bonds : angle 4.97432 ( 813) link_BETA1-4 : bond 0.00408 ( 2) link_BETA1-4 : angle 2.47610 ( 6) link_NAG-ASN : bond 0.00138 ( 2) link_NAG-ASN : angle 2.16826 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7645 (m-80) cc_final: 0.7341 (m-80) REVERT: A 420 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 478 SER cc_start: 0.7920 (p) cc_final: 0.7364 (t) REVERT: A 513 ILE cc_start: 0.7274 (mt) cc_final: 0.6940 (mp) REVERT: B 80 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6605 (ptm160) REVERT: B 87 MET cc_start: 0.6388 (mmm) cc_final: 0.5732 (mmm) REVERT: B 276 HIS cc_start: 0.4679 (OUTLIER) cc_final: 0.4064 (p90) REVERT: B 310 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 388 MET cc_start: 0.7093 (mtp) cc_final: 0.6745 (mtp) REVERT: B 436 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7879 (mtmm) REVERT: B 441 SER cc_start: 0.8094 (p) cc_final: 0.7812 (t) REVERT: B 561 ASP cc_start: 0.7156 (p0) cc_final: 0.6808 (t0) REVERT: B 624 MET cc_start: 0.7589 (mmm) cc_final: 0.7377 (mmt) outliers start: 25 outliers final: 19 residues processed: 182 average time/residue: 0.4445 time to fit residues: 87.9195 Evaluate side-chains 182 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN A 721 GLN B 176 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.235673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.203705 restraints weight = 11326.806| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 2.66 r_work: 0.4451 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 9599 Z= 0.223 Angle : 1.020 59.199 13061 Z= 0.554 Chirality : 0.047 0.423 1433 Planarity : 0.004 0.046 1650 Dihedral : 7.665 72.305 1375 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.13 % Favored : 93.61 % Rotamer: Outliers : 2.37 % Allowed : 22.16 % Favored : 75.47 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.25), residues: 1126 helix: 0.37 (0.27), residues: 374 sheet: -1.74 (0.50), residues: 114 loop : -0.77 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 595 TYR 0.032 0.001 TYR A 467 PHE 0.022 0.001 PHE B 400 TRP 0.031 0.002 TRP A 200 HIS 0.005 0.001 HIS B 262 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9585) covalent geometry : angle 1.01742 (13029) SS BOND : bond 0.00312 ( 10) SS BOND : angle 1.15186 ( 20) hydrogen bonds : bond 0.03926 ( 294) hydrogen bonds : angle 4.97291 ( 813) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 2.47465 ( 6) link_NAG-ASN : bond 0.00136 ( 2) link_NAG-ASN : angle 2.16760 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3116.74 seconds wall clock time: 53 minutes 54.56 seconds (3234.56 seconds total)