Starting phenix.real_space_refine on Wed Feb 4 09:06:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w1z_43735/02_2026/8w1z_43735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w1z_43735/02_2026/8w1z_43735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w1z_43735/02_2026/8w1z_43735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w1z_43735/02_2026/8w1z_43735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w1z_43735/02_2026/8w1z_43735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w1z_43735/02_2026/8w1z_43735.map" } resolution = 3.79 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= 0.001 sd= 0.022 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 71 5.16 5 C 6185 2.51 5 N 1573 2.21 5 O 1714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9543 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4773 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 23, 'TRANS': 580} Chain breaks: 1 Chain: "B" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4658 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 21, 'TRANS': 566} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.29, per 1000 atoms: 0.24 Number of scatterers: 9543 At special positions: 0 Unit cell: (84.8, 126.14, 138.86, 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 71 16.00 O 1714 8.00 N 1573 7.00 C 6185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 69 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 413 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 397 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 69 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 413 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 584 " 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 NAG-ASN " NAG A 801 " - " ASN A 80 " " NAG A 802 " - " ASN A 92 " " NAG A 803 " - " ASN A 155 " " NAG B 801 " - " ASN B 80 " " NAG B 802 " - " ASN B 92 " " NAG B 803 " - " ASN B 155 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 563.1 milliseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 49.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.203A pdb=" N LYS A 105 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.554A pdb=" N PHE A 297 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.972A pdb=" N CYS A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 removed outlier: 4.776A pdb=" N THR A 321 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET A 322 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 324 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.501A pdb=" N ARG A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 4.037A pdb=" N ASN A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 458 Processing helix chain 'A' and resid 463 through 494 removed outlier: 4.447A pdb=" N LEU A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.576A pdb=" N HIS A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 545 removed outlier: 3.601A pdb=" N ARG A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 570 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 592 through 626 Processing helix chain 'A' and resid 632 through 660 removed outlier: 3.847A pdb=" N LEU A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) Proline residue: A 652 - end of helix removed outlier: 3.530A pdb=" N PHE A 655 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 692 removed outlier: 4.295A pdb=" N PHE A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Proline residue: A 681 - end of helix Proline residue: A 688 - end of helix Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.950A pdb=" N GLU B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.589A pdb=" N LYS B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 131 Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.626A pdb=" N LYS B 276 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.240A pdb=" N CYS B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 326 through 343 removed outlier: 3.922A pdb=" N ARG B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 Processing helix chain 'B' and resid 429 through 458 Processing helix chain 'B' and resid 463 through 493 Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.876A pdb=" N TRP B 504 " --> pdb=" O HIS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 545 removed outlier: 3.718A pdb=" N ALA B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 543 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 570 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 591 through 626 removed outlier: 3.620A pdb=" N SER B 596 " --> pdb=" O ILE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 651 removed outlier: 3.674A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.964A pdb=" N PHE B 655 " --> pdb=" O PHE B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 692 removed outlier: 4.399A pdb=" N PHE B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Proline residue: B 681 - end of helix Proline residue: B 688 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 removed outlier: 8.460A pdb=" N TYR A 89 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS A 67 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS A 91 " --> pdb=" O CYS A 67 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS A 69 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 112 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N VAL A 140 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 114 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 137 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS A 165 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 139 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ARG A 187 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 211 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP A 189 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N LYS A 207 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N LYS A 233 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 209 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LYS A 235 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 211 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N PHE A 231 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A 259 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N LYS A 233 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN A 257 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE A 281 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A 259 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 280 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.542A pdb=" N ASP A 124 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE A 123 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 198 removed outlier: 3.659A pdb=" N ILE A 198 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 221 " --> pdb=" O SER A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 204 removed outlier: 6.580A pdb=" N VAL A 203 " --> pdb=" O THR A 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 57 removed outlier: 6.735A pdb=" N LEU B 88 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP B 115 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU B 90 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 137 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LYS B 165 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 139 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 162 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 211 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 280 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.024A pdb=" N ILE B 123 " --> pdb=" O SER B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 446 hydrogen bonds defined for protein. 1305 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: 1.01 Time building geometry restraints manager: 0.99 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: 2964 1.34 - 1.46: 2250 1.46 - 1.58: 4433 1.58 - 1.70: 0 1.70 - 1.82: 109 Bond restraints: 9756 Sorted by residual: bond pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.27e-01 bond pdb=" C ILE A 392 " pdb=" N GLY A 393 " ideal model delta sigma weight residual 1.321 1.332 -0.011 1.12e-02 7.97e+03 9.21e-01 bond pdb=" N GLY A 63 " pdb=" CA GLY A 63 " ideal model delta sigma weight residual 1.449 1.463 -0.013 1.45e-02 4.76e+03 8.54e-01 bond pdb=" CA LEU B 269 " pdb=" C LEU B 269 " ideal model delta sigma weight residual 1.524 1.517 0.007 8.10e-03 1.52e+04 7.42e-01 bond pdb=" CA TYR B 497 " pdb=" C TYR B 497 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.34e-02 5.57e+03 6.93e-01 ... (remaining 9751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 13013 1.85 - 3.70: 180 3.70 - 5.55: 26 5.55 - 7.40: 4 7.40 - 9.25: 2 Bond angle restraints: 13225 Sorted by residual: angle pdb=" C ASP B 284 " pdb=" N VAL B 285 " pdb=" CA VAL B 285 " ideal model delta sigma weight residual 122.60 119.50 3.10 6.80e-01 2.16e+00 2.08e+01 angle pdb=" C HIS A 91 " pdb=" N ASN A 92 " pdb=" CA ASN A 92 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.49e+00 angle pdb=" N ILE A 426 " pdb=" CA ILE A 426 " pdb=" C ILE A 426 " ideal model delta sigma weight residual 111.67 108.84 2.83 9.50e-01 1.11e+00 8.88e+00 angle pdb=" C SER A 214 " pdb=" N GLU A 215 " pdb=" CA GLU A 215 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.20e+00 angle pdb=" CA ASN A 92 " pdb=" CB ASN A 92 " pdb=" CG ASN A 92 " ideal model delta sigma weight residual 112.60 115.25 -2.65 1.00e+00 1.00e+00 7.01e+00 ... (remaining 13220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.39: 5705 23.39 - 46.77: 237 46.77 - 70.16: 45 70.16 - 93.54: 8 93.54 - 116.93: 1 Dihedral angle restraints: 5996 sinusoidal: 2501 harmonic: 3495 Sorted by residual: dihedral pdb=" CA PHE A 678 " pdb=" C PHE A 678 " pdb=" N PHE A 679 " pdb=" CA PHE A 679 " ideal model delta harmonic sigma weight residual -180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA TYR B 497 " pdb=" C TYR B 497 " pdb=" N TYR B 498 " pdb=" CA TYR B 498 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TRP B 650 " pdb=" C TRP B 650 " pdb=" N PHE B 651 " pdb=" CA PHE B 651 " ideal model delta harmonic sigma weight residual -180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 5993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1181 0.044 - 0.087: 275 0.087 - 0.131: 84 0.131 - 0.174: 7 0.174 - 0.218: 1 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CA ASN A 92 " pdb=" N ASN A 92 " pdb=" C ASN A 92 " pdb=" CB ASN A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 155 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 92 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1545 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 680 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 681 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 285 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO B 286 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 291 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A 292 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " 0.016 5.00e-02 4.00e+02 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 136 2.66 - 3.22: 9621 3.22 - 3.78: 15002 3.78 - 4.34: 19922 4.34 - 4.90: 32117 Nonbonded interactions: 76798 Sorted by model distance: nonbonded pdb=" OG SER A 399 " pdb=" OE1 GLU A 402 " model vdw 2.099 3.040 nonbonded pdb=" OD1 ASN A 471 " pdb=" OG SER A 527 " model vdw 2.128 3.040 nonbonded pdb=" O PRO B 240 " pdb=" OG SER B 265 " model vdw 2.152 3.040 nonbonded pdb=" O PHE A 593 " pdb=" OG SER A 596 " model vdw 2.224 3.040 nonbonded pdb=" OG SER B 536 " pdb=" OG SER B 615 " model vdw 2.242 3.040 ... (remaining 76793 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 'A' and (resid 41 through 343 or resid 399 through 660 or resid 670 throu \ gh 803)) selection = (chain 'B' and resid 41 through 803) } 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 group one per residue 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: 1.520 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: 0.050 Process input model: 9.370 Find NCS groups from input model: 0.170 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 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 : 0.002 0.023 9775 Z= 0.126 Angle : 0.584 9.830 13269 Z= 0.315 Chirality : 0.041 0.218 1548 Planarity : 0.004 0.036 1632 Dihedral : 12.957 116.927 3693 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.25 % Rotamer: Outliers : 6.10 % Allowed : 7.72 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1182 helix: 1.55 (0.23), residues: 502 sheet: -1.04 (0.47), residues: 117 loop : -1.39 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 158 TYR 0.011 0.001 TYR B 328 PHE 0.016 0.001 PHE B 685 TRP 0.007 0.001 TRP B 561 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9756) covalent geometry : angle 0.57042 (13225) SS BOND : bond 0.00225 ( 13) SS BOND : angle 0.73382 ( 26) hydrogen bonds : bond 0.13200 ( 446) hydrogen bonds : angle 5.59219 ( 1305) link_NAG-ASN : bond 0.00327 ( 6) link_NAG-ASN : angle 3.44417 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8259 (pt) cc_final: 0.7572 (pt) REVERT: A 115 ASP cc_start: 0.7103 (p0) cc_final: 0.6651 (p0) REVERT: A 120 LEU cc_start: 0.6766 (mt) cc_final: 0.6530 (tt) REVERT: A 121 GLU cc_start: 0.7213 (tp30) cc_final: 0.6946 (tp30) REVERT: A 151 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7860 (mmtm) REVERT: A 165 LYS cc_start: 0.8174 (pttt) cc_final: 0.7852 (pttt) REVERT: A 177 MET cc_start: 0.8106 (tpp) cc_final: 0.7686 (tpt) REVERT: A 215 GLU cc_start: 0.7597 (mp0) cc_final: 0.7281 (mp0) REVERT: A 216 ASN cc_start: 0.7356 (m-40) cc_final: 0.6968 (m-40) REVERT: A 224 TYR cc_start: 0.7181 (m-80) cc_final: 0.6907 (m-80) REVERT: A 277 LEU cc_start: 0.8178 (mt) cc_final: 0.7959 (mp) REVERT: A 290 SER cc_start: 0.8391 (t) cc_final: 0.7817 (p) REVERT: A 414 TYR cc_start: 0.5622 (OUTLIER) cc_final: 0.5234 (t80) REVERT: A 418 ASP cc_start: 0.7718 (p0) cc_final: 0.7459 (p0) REVERT: A 432 LEU cc_start: 0.8580 (mt) cc_final: 0.8305 (mm) REVERT: A 464 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6872 (ppp) REVERT: A 477 MET cc_start: 0.6768 (tpt) cc_final: 0.6449 (tpt) REVERT: A 505 GLN cc_start: 0.6933 (tt0) cc_final: 0.6627 (tt0) REVERT: A 567 MET cc_start: 0.8113 (tpp) cc_final: 0.7810 (mmm) REVERT: A 595 LYS cc_start: 0.7459 (mmmt) cc_final: 0.7151 (mmmt) REVERT: A 667 LEU cc_start: 0.2016 (OUTLIER) cc_final: 0.1711 (tt) REVERT: B 44 MET cc_start: 0.7448 (mtt) cc_final: 0.6977 (mtm) REVERT: B 123 ILE cc_start: 0.7771 (mt) cc_final: 0.7364 (mp) REVERT: B 166 ASN cc_start: 0.7944 (m-40) cc_final: 0.6879 (t0) REVERT: B 167 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7091 (m110) REVERT: B 194 LYS cc_start: 0.7250 (mptp) cc_final: 0.6588 (mptp) REVERT: B 198 ILE cc_start: 0.7289 (mm) cc_final: 0.7080 (tt) REVERT: B 217 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.5342 (tppt) REVERT: B 219 ILE cc_start: 0.7498 (tp) cc_final: 0.7148 (tp) REVERT: B 220 GLU cc_start: 0.6206 (tm-30) cc_final: 0.5899 (tm-30) REVERT: B 276 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7635 (mmtt) REVERT: B 315 LYS cc_start: 0.7153 (ptmm) cc_final: 0.6756 (mttt) REVERT: B 420 LEU cc_start: 0.7288 (mt) cc_final: 0.6982 (mt) REVERT: B 424 GLU cc_start: 0.6335 (mt-10) cc_final: 0.4703 (mt-10) REVERT: B 447 ASN cc_start: 0.7133 (m-40) cc_final: 0.6725 (m110) REVERT: B 468 TYR cc_start: 0.6767 (m-10) cc_final: 0.6277 (m-10) REVERT: B 469 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6540 (mmt) REVERT: B 492 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7709 (mmmt) REVERT: B 531 ILE cc_start: 0.7321 (tp) cc_final: 0.7083 (mt) REVERT: B 557 MET cc_start: 0.7003 (tmm) cc_final: 0.6678 (tmm) REVERT: B 599 ILE cc_start: 0.7672 (tp) cc_final: 0.7419 (tp) outliers start: 64 outliers final: 27 residues processed: 303 average time/residue: 0.0862 time to fit residues: 36.1781 Evaluate side-chains 251 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 683 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN A 239 ASN A 329 GLN A 331 ASN A 421 ASN A 425 ASN B 64 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.192363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.155660 restraints weight = 15410.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160198 restraints weight = 9199.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163279 restraints weight = 6420.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.165205 restraints weight = 5039.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.166324 restraints weight = 4306.709| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9775 Z= 0.178 Angle : 0.695 12.107 13269 Z= 0.354 Chirality : 0.045 0.214 1548 Planarity : 0.005 0.061 1632 Dihedral : 9.222 59.895 1532 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 5.82 % Allowed : 13.82 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1182 helix: 1.30 (0.22), residues: 521 sheet: -0.85 (0.52), residues: 93 loop : -1.38 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 243 TYR 0.025 0.002 TYR A 498 PHE 0.016 0.002 PHE B 656 TRP 0.013 0.001 TRP B 508 HIS 0.007 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9756) covalent geometry : angle 0.67462 (13225) SS BOND : bond 0.00773 ( 13) SS BOND : angle 2.17531 ( 26) hydrogen bonds : bond 0.05049 ( 446) hydrogen bonds : angle 5.00475 ( 1305) link_NAG-ASN : bond 0.00282 ( 6) link_NAG-ASN : angle 3.80725 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6669 (ttm) cc_final: 0.6088 (ptp) REVERT: A 115 ASP cc_start: 0.7034 (p0) cc_final: 0.6514 (p0) REVERT: A 141 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7531 (mmpt) REVERT: A 151 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7872 (mmtm) REVERT: A 224 TYR cc_start: 0.7354 (m-80) cc_final: 0.6951 (m-80) REVERT: A 276 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7704 (mmtt) REVERT: A 277 LEU cc_start: 0.8213 (mt) cc_final: 0.7984 (mp) REVERT: A 290 SER cc_start: 0.8404 (t) cc_final: 0.7880 (p) REVERT: A 414 TYR cc_start: 0.5641 (OUTLIER) cc_final: 0.5310 (t80) REVERT: A 447 ASN cc_start: 0.6386 (OUTLIER) cc_final: 0.5595 (t0) REVERT: A 464 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6941 (ppp) REVERT: A 477 MET cc_start: 0.6861 (tpt) cc_final: 0.6372 (tpt) REVERT: A 488 ILE cc_start: 0.7912 (pt) cc_final: 0.7690 (pt) REVERT: A 566 ILE cc_start: 0.7553 (tt) cc_final: 0.7255 (mt) REVERT: A 570 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7814 (tp) REVERT: A 595 LYS cc_start: 0.7496 (mmmt) cc_final: 0.7131 (mmmt) REVERT: B 44 MET cc_start: 0.7255 (mtt) cc_final: 0.6881 (mtm) REVERT: B 84 ASP cc_start: 0.6277 (p0) cc_final: 0.5909 (p0) REVERT: B 166 ASN cc_start: 0.7964 (m-40) cc_final: 0.7197 (t0) REVERT: B 176 ARG cc_start: 0.6615 (ttt180) cc_final: 0.6402 (ttt180) REVERT: B 194 LYS cc_start: 0.7156 (mptp) cc_final: 0.6686 (mptp) REVERT: B 206 VAL cc_start: 0.7415 (t) cc_final: 0.6861 (p) REVERT: B 219 ILE cc_start: 0.7499 (tp) cc_final: 0.7148 (tp) REVERT: B 231 PHE cc_start: 0.8023 (m-10) cc_final: 0.7680 (m-10) REVERT: B 315 LYS cc_start: 0.7202 (ptmm) cc_final: 0.6878 (mttp) REVERT: B 433 ARG cc_start: 0.7541 (ttp-170) cc_final: 0.7331 (ttp-170) REVERT: B 437 TRP cc_start: 0.7406 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: B 492 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7723 (mmmt) REVERT: B 531 ILE cc_start: 0.7532 (tp) cc_final: 0.7214 (mt) REVERT: B 557 MET cc_start: 0.6803 (tmm) cc_final: 0.6564 (tmm) REVERT: B 558 ILE cc_start: 0.7734 (mm) cc_final: 0.7431 (pt) REVERT: B 572 TRP cc_start: 0.7923 (m-10) cc_final: 0.7560 (m-10) REVERT: B 599 ILE cc_start: 0.7705 (tp) cc_final: 0.7434 (tp) outliers start: 61 outliers final: 36 residues processed: 259 average time/residue: 0.0881 time to fit residues: 31.1339 Evaluate side-chains 248 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 572 TRP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 683 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN ** B 500 HIS ** 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 = 0.4387 r_free = 0.4387 target = 0.192327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155657 restraints weight = 15513.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.160222 restraints weight = 9225.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.163384 restraints weight = 6396.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.165202 restraints weight = 4972.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.166656 restraints weight = 4286.880| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9775 Z= 0.168 Angle : 0.668 12.772 13269 Z= 0.344 Chirality : 0.045 0.230 1548 Planarity : 0.004 0.050 1632 Dihedral : 8.565 59.940 1518 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 5.62 % Allowed : 15.82 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1182 helix: 1.23 (0.22), residues: 521 sheet: -0.94 (0.52), residues: 95 loop : -1.37 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 499 TYR 0.033 0.002 TYR B 616 PHE 0.018 0.001 PHE A 102 TRP 0.012 0.001 TRP B 508 HIS 0.005 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9756) covalent geometry : angle 0.64977 (13225) SS BOND : bond 0.00830 ( 13) SS BOND : angle 1.87172 ( 26) hydrogen bonds : bond 0.04909 ( 446) hydrogen bonds : angle 4.93279 ( 1305) link_NAG-ASN : bond 0.00244 ( 6) link_NAG-ASN : angle 3.74913 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7302 (ptpp) REVERT: A 70 MET cc_start: 0.6774 (ttm) cc_final: 0.6235 (ptt) REVERT: A 115 ASP cc_start: 0.6912 (p0) cc_final: 0.6558 (p0) REVERT: A 141 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7537 (mmpt) REVERT: A 151 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7860 (mmtm) REVERT: A 215 GLU cc_start: 0.7599 (mp0) cc_final: 0.7163 (mp0) REVERT: A 224 TYR cc_start: 0.7346 (m-80) cc_final: 0.6951 (m-80) REVERT: A 252 ASN cc_start: 0.7378 (t0) cc_final: 0.7159 (t0) REVERT: A 276 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7701 (mmtt) REVERT: A 290 SER cc_start: 0.8391 (t) cc_final: 0.7888 (p) REVERT: A 414 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.5327 (t80) REVERT: A 418 ASP cc_start: 0.7772 (p0) cc_final: 0.7365 (p0) REVERT: A 477 MET cc_start: 0.6796 (tpt) cc_final: 0.6345 (tpt) REVERT: A 566 ILE cc_start: 0.7480 (tt) cc_final: 0.7213 (mt) REVERT: A 595 LYS cc_start: 0.7503 (mmmt) cc_final: 0.7053 (mmmt) REVERT: B 44 MET cc_start: 0.7235 (mtt) cc_final: 0.6608 (mtm) REVERT: B 84 ASP cc_start: 0.6251 (p0) cc_final: 0.5598 (p0) REVERT: B 166 ASN cc_start: 0.7988 (m-40) cc_final: 0.7208 (t0) REVERT: B 176 ARG cc_start: 0.6448 (ttt180) cc_final: 0.6203 (ttt180) REVERT: B 194 LYS cc_start: 0.7168 (mptp) cc_final: 0.6664 (mptp) REVERT: B 206 VAL cc_start: 0.7389 (t) cc_final: 0.6871 (p) REVERT: B 217 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.5280 (tppt) REVERT: B 219 ILE cc_start: 0.7509 (tp) cc_final: 0.7152 (tp) REVERT: B 220 GLU cc_start: 0.6220 (tm-30) cc_final: 0.6012 (tm-30) REVERT: B 315 LYS cc_start: 0.7289 (ptmm) cc_final: 0.6762 (mttt) REVERT: B 433 ARG cc_start: 0.7585 (ttp-170) cc_final: 0.7383 (ttp-170) REVERT: B 437 TRP cc_start: 0.7365 (OUTLIER) cc_final: 0.6548 (m-10) REVERT: B 464 MET cc_start: 0.4299 (ppp) cc_final: 0.4092 (ppp) REVERT: B 481 ILE cc_start: 0.6813 (pt) cc_final: 0.6516 (tp) REVERT: B 492 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7746 (mmmt) REVERT: B 531 ILE cc_start: 0.7598 (tp) cc_final: 0.7275 (mt) REVERT: B 557 MET cc_start: 0.6843 (tmm) cc_final: 0.6569 (tmm) REVERT: B 558 ILE cc_start: 0.7745 (mm) cc_final: 0.7401 (pt) REVERT: B 572 TRP cc_start: 0.7957 (m-10) cc_final: 0.7700 (m-10) outliers start: 59 outliers final: 37 residues processed: 258 average time/residue: 0.0965 time to fit residues: 33.8338 Evaluate side-chains 250 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 572 TRP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 683 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.191509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155046 restraints weight = 15608.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.159670 restraints weight = 9256.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.162704 restraints weight = 6433.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.164934 restraints weight = 5039.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.166021 restraints weight = 4259.650| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9775 Z= 0.174 Angle : 0.665 10.344 13269 Z= 0.342 Chirality : 0.044 0.213 1548 Planarity : 0.004 0.049 1632 Dihedral : 8.339 58.995 1513 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.82 % Rotamer: Outliers : 5.82 % Allowed : 17.16 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1182 helix: 1.15 (0.22), residues: 527 sheet: -1.00 (0.58), residues: 77 loop : -1.49 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.025 0.002 TYR B 616 PHE 0.017 0.001 PHE A 689 TRP 0.013 0.001 TRP A 561 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9756) covalent geometry : angle 0.64565 (13225) SS BOND : bond 0.00447 ( 13) SS BOND : angle 1.98470 ( 26) hydrogen bonds : bond 0.04833 ( 446) hydrogen bonds : angle 4.90582 ( 1305) link_NAG-ASN : bond 0.00297 ( 6) link_NAG-ASN : angle 3.71701 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7285 (ptpp) REVERT: A 70 MET cc_start: 0.6656 (ttm) cc_final: 0.6120 (ptt) REVERT: A 115 ASP cc_start: 0.6932 (p0) cc_final: 0.6553 (p0) REVERT: A 141 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7554 (mmpt) REVERT: A 151 LYS cc_start: 0.8082 (mmtm) cc_final: 0.7862 (mmtm) REVERT: A 224 TYR cc_start: 0.7190 (m-80) cc_final: 0.6888 (m-80) REVERT: A 252 ASN cc_start: 0.7417 (t0) cc_final: 0.7133 (t0) REVERT: A 276 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7712 (mmtt) REVERT: A 290 SER cc_start: 0.8401 (t) cc_final: 0.7911 (p) REVERT: A 414 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.5340 (t80) REVERT: A 418 ASP cc_start: 0.7761 (p0) cc_final: 0.7488 (p0) REVERT: A 477 MET cc_start: 0.6792 (tpt) cc_final: 0.6333 (tpt) REVERT: A 526 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7646 (tt) REVERT: A 566 ILE cc_start: 0.7486 (tt) cc_final: 0.7223 (mt) REVERT: A 570 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7807 (tp) REVERT: A 595 LYS cc_start: 0.7493 (mmmt) cc_final: 0.7032 (mmmt) REVERT: B 44 MET cc_start: 0.7232 (mtt) cc_final: 0.6609 (mtm) REVERT: B 84 ASP cc_start: 0.6338 (p0) cc_final: 0.5715 (p0) REVERT: B 166 ASN cc_start: 0.8027 (m-40) cc_final: 0.7239 (t0) REVERT: B 194 LYS cc_start: 0.7159 (mptp) cc_final: 0.6676 (mptp) REVERT: B 219 ILE cc_start: 0.7512 (tp) cc_final: 0.7160 (tp) REVERT: B 220 GLU cc_start: 0.6246 (tm-30) cc_final: 0.6003 (tm-30) REVERT: B 433 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7392 (ttp-170) REVERT: B 440 CYS cc_start: 0.7956 (p) cc_final: 0.7662 (p) REVERT: B 464 MET cc_start: 0.4360 (ppp) cc_final: 0.4079 (ppp) REVERT: B 469 MET cc_start: 0.6878 (mmm) cc_final: 0.6435 (mmm) REVERT: B 481 ILE cc_start: 0.6804 (pt) cc_final: 0.6491 (tp) REVERT: B 492 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7782 (mmmt) REVERT: B 531 ILE cc_start: 0.7615 (tp) cc_final: 0.7329 (mt) REVERT: B 557 MET cc_start: 0.6687 (tmm) cc_final: 0.6435 (tmm) REVERT: B 563 PHE cc_start: 0.7347 (t80) cc_final: 0.7133 (t80) REVERT: B 572 TRP cc_start: 0.7988 (m-10) cc_final: 0.7562 (m100) outliers start: 61 outliers final: 42 residues processed: 255 average time/residue: 0.0801 time to fit residues: 28.1284 Evaluate side-chains 254 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 572 TRP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 683 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 113 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 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 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN ** B 500 HIS ** 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 = 0.4383 r_free = 0.4383 target = 0.191854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155582 restraints weight = 15551.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160243 restraints weight = 9203.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.163043 restraints weight = 6401.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.165250 restraints weight = 5086.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.166473 restraints weight = 4288.178| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9775 Z= 0.153 Angle : 0.653 12.229 13269 Z= 0.335 Chirality : 0.043 0.216 1548 Planarity : 0.004 0.046 1632 Dihedral : 8.167 58.452 1510 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 93.99 % Rotamer: Outliers : 5.72 % Allowed : 18.49 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.24), residues: 1182 helix: 1.20 (0.22), residues: 528 sheet: -1.10 (0.56), residues: 87 loop : -1.50 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.021 0.001 TYR B 616 PHE 0.021 0.001 PHE A 102 TRP 0.014 0.001 TRP A 561 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9756) covalent geometry : angle 0.63375 (13225) SS BOND : bond 0.00703 ( 13) SS BOND : angle 1.98527 ( 26) hydrogen bonds : bond 0.04519 ( 446) hydrogen bonds : angle 4.77519 ( 1305) link_NAG-ASN : bond 0.00293 ( 6) link_NAG-ASN : angle 3.70128 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6746 (ttm) cc_final: 0.6187 (ptt) REVERT: A 115 ASP cc_start: 0.6877 (p0) cc_final: 0.6532 (p0) REVERT: A 141 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7529 (mmpt) REVERT: A 151 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7875 (mmtm) REVERT: A 177 MET cc_start: 0.8183 (tpp) cc_final: 0.7518 (mmm) REVERT: A 204 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6972 (ttm-80) REVERT: A 224 TYR cc_start: 0.7409 (m-80) cc_final: 0.7003 (m-80) REVERT: A 252 ASN cc_start: 0.7430 (t0) cc_final: 0.7179 (t0) REVERT: A 265 SER cc_start: 0.7607 (m) cc_final: 0.6841 (t) REVERT: A 276 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7695 (mmtt) REVERT: A 290 SER cc_start: 0.8401 (t) cc_final: 0.7925 (p) REVERT: A 414 TYR cc_start: 0.5663 (OUTLIER) cc_final: 0.5355 (t80) REVERT: A 418 ASP cc_start: 0.7736 (p0) cc_final: 0.7517 (p0) REVERT: A 447 ASN cc_start: 0.6463 (OUTLIER) cc_final: 0.5645 (t0) REVERT: A 472 MET cc_start: 0.7542 (tpt) cc_final: 0.7093 (tpt) REVERT: A 477 MET cc_start: 0.6759 (tpt) cc_final: 0.6370 (tpt) REVERT: A 488 ILE cc_start: 0.7895 (pt) cc_final: 0.7646 (pt) REVERT: A 526 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7630 (tt) REVERT: A 566 ILE cc_start: 0.7505 (tt) cc_final: 0.7177 (mt) REVERT: A 570 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7797 (tp) REVERT: A 595 LYS cc_start: 0.7433 (mmmt) cc_final: 0.6986 (mmmt) REVERT: B 44 MET cc_start: 0.7084 (mtt) cc_final: 0.6552 (mtm) REVERT: B 84 ASP cc_start: 0.6310 (p0) cc_final: 0.5705 (p0) REVERT: B 166 ASN cc_start: 0.8050 (m-40) cc_final: 0.7246 (t0) REVERT: B 194 LYS cc_start: 0.7092 (mptp) cc_final: 0.6601 (mptp) REVERT: B 219 ILE cc_start: 0.7500 (tp) cc_final: 0.7164 (tp) REVERT: B 220 GLU cc_start: 0.6212 (tm-30) cc_final: 0.5959 (tm-30) REVERT: B 338 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7384 (ttp80) REVERT: B 440 CYS cc_start: 0.7922 (p) cc_final: 0.7632 (p) REVERT: B 469 MET cc_start: 0.6782 (mmm) cc_final: 0.6374 (mmm) REVERT: B 481 ILE cc_start: 0.6783 (pt) cc_final: 0.6525 (tp) REVERT: B 492 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7806 (mmmt) REVERT: B 531 ILE cc_start: 0.7617 (tp) cc_final: 0.7366 (mt) REVERT: B 557 MET cc_start: 0.6840 (tmm) cc_final: 0.6605 (tmm) REVERT: B 563 PHE cc_start: 0.7329 (t80) cc_final: 0.7104 (t80) REVERT: B 572 TRP cc_start: 0.7994 (m-10) cc_final: 0.7578 (m100) outliers start: 60 outliers final: 39 residues processed: 258 average time/residue: 0.0919 time to fit residues: 32.6434 Evaluate side-chains 254 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 572 TRP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 683 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 114 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 500 HIS ** 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 = 0.4388 r_free = 0.4388 target = 0.192422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.156139 restraints weight = 15458.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.160660 restraints weight = 9206.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.163830 restraints weight = 6440.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165944 restraints weight = 4998.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.167088 restraints weight = 4255.574| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9775 Z= 0.151 Angle : 0.657 12.531 13269 Z= 0.334 Chirality : 0.044 0.226 1548 Planarity : 0.004 0.045 1632 Dihedral : 8.050 59.085 1510 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.74 % Rotamer: Outliers : 5.62 % Allowed : 19.26 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1182 helix: 1.24 (0.22), residues: 523 sheet: -1.02 (0.58), residues: 77 loop : -1.48 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 243 TYR 0.018 0.001 TYR B 498 PHE 0.023 0.001 PHE B 606 TRP 0.015 0.001 TRP A 561 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9756) covalent geometry : angle 0.63899 (13225) SS BOND : bond 0.00367 ( 13) SS BOND : angle 1.71350 ( 26) hydrogen bonds : bond 0.04423 ( 446) hydrogen bonds : angle 4.70976 ( 1305) link_NAG-ASN : bond 0.00272 ( 6) link_NAG-ASN : angle 3.71640 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6778 (ttm) cc_final: 0.6364 (ptt) REVERT: A 115 ASP cc_start: 0.6882 (p0) cc_final: 0.6551 (p0) REVERT: A 141 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7522 (mmpt) REVERT: A 151 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7878 (mmtm) REVERT: A 177 MET cc_start: 0.8217 (tpp) cc_final: 0.7562 (mmm) REVERT: A 204 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6950 (ttm-80) REVERT: A 224 TYR cc_start: 0.7376 (m-80) cc_final: 0.6960 (m-80) REVERT: A 252 ASN cc_start: 0.7418 (t0) cc_final: 0.7187 (t0) REVERT: A 265 SER cc_start: 0.7634 (m) cc_final: 0.6851 (t) REVERT: A 290 SER cc_start: 0.8342 (t) cc_final: 0.7858 (p) REVERT: A 414 TYR cc_start: 0.5619 (OUTLIER) cc_final: 0.5309 (t80) REVERT: A 418 ASP cc_start: 0.7742 (p0) cc_final: 0.7541 (p0) REVERT: A 472 MET cc_start: 0.7551 (tpt) cc_final: 0.7092 (tpt) REVERT: A 477 MET cc_start: 0.6810 (tpt) cc_final: 0.6346 (tpt) REVERT: A 488 ILE cc_start: 0.7912 (pt) cc_final: 0.7691 (pt) REVERT: A 526 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7631 (tt) REVERT: A 535 MET cc_start: 0.5185 (tpt) cc_final: 0.4982 (tpt) REVERT: A 566 ILE cc_start: 0.7437 (tt) cc_final: 0.7173 (mt) REVERT: A 570 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 595 LYS cc_start: 0.7449 (mmmt) cc_final: 0.7008 (mmmt) REVERT: A 655 PHE cc_start: 0.5437 (OUTLIER) cc_final: 0.5121 (t80) REVERT: B 44 MET cc_start: 0.6996 (mtt) cc_final: 0.6216 (mtm) REVERT: B 84 ASP cc_start: 0.6333 (p0) cc_final: 0.5747 (p0) REVERT: B 166 ASN cc_start: 0.8087 (m-40) cc_final: 0.7277 (t0) REVERT: B 194 LYS cc_start: 0.7073 (mptp) cc_final: 0.6565 (mptp) REVERT: B 219 ILE cc_start: 0.7498 (tp) cc_final: 0.7155 (tp) REVERT: B 220 GLU cc_start: 0.6198 (tm-30) cc_final: 0.5933 (tm-30) REVERT: B 338 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7298 (ttp80) REVERT: B 440 CYS cc_start: 0.7918 (p) cc_final: 0.7638 (p) REVERT: B 464 MET cc_start: 0.4246 (ppp) cc_final: 0.3908 (ppp) REVERT: B 468 TYR cc_start: 0.6448 (m-10) cc_final: 0.5862 (m-10) REVERT: B 469 MET cc_start: 0.6761 (mmm) cc_final: 0.6373 (mmm) REVERT: B 481 ILE cc_start: 0.6820 (pt) cc_final: 0.6574 (tp) REVERT: B 492 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7783 (mmmt) REVERT: B 531 ILE cc_start: 0.7638 (tp) cc_final: 0.7372 (mt) REVERT: B 563 PHE cc_start: 0.7333 (t80) cc_final: 0.7096 (t80) REVERT: B 572 TRP cc_start: 0.7988 (m-10) cc_final: 0.7593 (m100) REVERT: B 622 MET cc_start: 0.6584 (mmm) cc_final: 0.5971 (mmm) REVERT: B 685 PHE cc_start: 0.4024 (OUTLIER) cc_final: 0.3803 (p90) outliers start: 59 outliers final: 43 residues processed: 252 average time/residue: 0.0861 time to fit residues: 29.8821 Evaluate side-chains 256 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 572 TRP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 685 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** 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 = 0.4367 r_free = 0.4367 target = 0.190706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.154397 restraints weight = 15581.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158800 restraints weight = 9360.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161803 restraints weight = 6580.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.163956 restraints weight = 5164.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.165047 restraints weight = 4377.598| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9775 Z= 0.200 Angle : 0.685 10.663 13269 Z= 0.351 Chirality : 0.045 0.218 1548 Planarity : 0.004 0.051 1632 Dihedral : 8.185 59.590 1509 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 5.91 % Allowed : 19.35 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.44 (0.24), residues: 1182 helix: 1.08 (0.22), residues: 524 sheet: -1.23 (0.57), residues: 77 loop : -1.49 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 243 TYR 0.017 0.002 TYR A 498 PHE 0.018 0.002 PHE B 656 TRP 0.025 0.002 TRP A 561 HIS 0.009 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9756) covalent geometry : angle 0.66787 (13225) SS BOND : bond 0.00625 ( 13) SS BOND : angle 1.60527 ( 26) hydrogen bonds : bond 0.04728 ( 446) hydrogen bonds : angle 4.86042 ( 1305) link_NAG-ASN : bond 0.00257 ( 6) link_NAG-ASN : angle 3.77677 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 208 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6776 (ttm) cc_final: 0.6320 (ptt) REVERT: A 115 ASP cc_start: 0.6869 (p0) cc_final: 0.6512 (p0) REVERT: A 141 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7548 (mmpt) REVERT: A 151 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7871 (mmtm) REVERT: A 204 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6959 (ttm-80) REVERT: A 224 TYR cc_start: 0.7331 (m-80) cc_final: 0.6923 (m-80) REVERT: A 252 ASN cc_start: 0.7512 (t0) cc_final: 0.7265 (t0) REVERT: A 289 LYS cc_start: 0.7996 (mmtm) cc_final: 0.7636 (mmtm) REVERT: A 290 SER cc_start: 0.8396 (t) cc_final: 0.7923 (p) REVERT: A 414 TYR cc_start: 0.5657 (OUTLIER) cc_final: 0.5379 (t80) REVERT: A 472 MET cc_start: 0.7610 (tpt) cc_final: 0.7214 (tpt) REVERT: A 477 MET cc_start: 0.6802 (tpt) cc_final: 0.6383 (tpt) REVERT: A 488 ILE cc_start: 0.7885 (pt) cc_final: 0.7645 (pt) REVERT: A 526 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7652 (tt) REVERT: A 566 ILE cc_start: 0.7491 (tt) cc_final: 0.7222 (mt) REVERT: A 595 LYS cc_start: 0.7458 (mmmt) cc_final: 0.7016 (mmmt) REVERT: A 646 ASP cc_start: 0.6258 (m-30) cc_final: 0.5635 (p0) REVERT: A 655 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.5079 (t80) REVERT: B 44 MET cc_start: 0.6983 (mtt) cc_final: 0.6194 (mtm) REVERT: B 84 ASP cc_start: 0.6356 (p0) cc_final: 0.5757 (p0) REVERT: B 166 ASN cc_start: 0.8205 (m-40) cc_final: 0.7384 (t0) REVERT: B 194 LYS cc_start: 0.7111 (mptp) cc_final: 0.6620 (mptp) REVERT: B 217 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.7015 (mmmt) REVERT: B 219 ILE cc_start: 0.7526 (tp) cc_final: 0.7178 (tp) REVERT: B 220 GLU cc_start: 0.6230 (tm-30) cc_final: 0.5954 (tm-30) REVERT: B 338 ARG cc_start: 0.7493 (ttp-170) cc_final: 0.7200 (ttp80) REVERT: B 440 CYS cc_start: 0.7913 (p) cc_final: 0.7673 (p) REVERT: B 464 MET cc_start: 0.4201 (ppp) cc_final: 0.3940 (ppp) REVERT: B 468 TYR cc_start: 0.6553 (m-10) cc_final: 0.5995 (m-10) REVERT: B 469 MET cc_start: 0.6806 (mmm) cc_final: 0.6382 (mmm) REVERT: B 481 ILE cc_start: 0.6907 (pt) cc_final: 0.6646 (tp) REVERT: B 492 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7914 (mmmt) REVERT: B 531 ILE cc_start: 0.7669 (tp) cc_final: 0.7426 (mt) REVERT: B 572 TRP cc_start: 0.8020 (m-10) cc_final: 0.7642 (m100) REVERT: B 622 MET cc_start: 0.6588 (mmm) cc_final: 0.5983 (mmm) outliers start: 62 outliers final: 45 residues processed: 251 average time/residue: 0.0887 time to fit residues: 30.8061 Evaluate side-chains 255 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 572 TRP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 683 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 500 HIS ** 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 = 0.4374 r_free = 0.4374 target = 0.191368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154878 restraints weight = 15579.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159367 restraints weight = 9381.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.162577 restraints weight = 6547.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.164303 restraints weight = 5107.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165839 restraints weight = 4387.467| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9775 Z= 0.179 Angle : 0.706 12.128 13269 Z= 0.362 Chirality : 0.044 0.217 1548 Planarity : 0.004 0.052 1632 Dihedral : 8.147 59.521 1509 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.24 % Allowed : 20.69 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.24), residues: 1182 helix: 1.09 (0.22), residues: 521 sheet: -1.08 (0.57), residues: 87 loop : -1.56 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.017 0.002 TYR A 498 PHE 0.023 0.002 PHE A 102 TRP 0.027 0.002 TRP A 561 HIS 0.007 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9756) covalent geometry : angle 0.68952 (13225) SS BOND : bond 0.00472 ( 13) SS BOND : angle 1.61826 ( 26) hydrogen bonds : bond 0.04659 ( 446) hydrogen bonds : angle 4.85650 ( 1305) link_NAG-ASN : bond 0.00270 ( 6) link_NAG-ASN : angle 3.77549 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6781 (ttm) cc_final: 0.6376 (ptt) REVERT: A 115 ASP cc_start: 0.6871 (p0) cc_final: 0.6498 (p0) REVERT: A 141 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7527 (mmpt) REVERT: A 151 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7865 (mmtm) REVERT: A 189 ASP cc_start: 0.6956 (t0) cc_final: 0.6423 (t0) REVERT: A 204 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6959 (ttm-80) REVERT: A 224 TYR cc_start: 0.7297 (m-80) cc_final: 0.6802 (m-80) REVERT: A 252 ASN cc_start: 0.7525 (t0) cc_final: 0.7253 (t0) REVERT: A 290 SER cc_start: 0.8413 (t) cc_final: 0.7942 (p) REVERT: A 414 TYR cc_start: 0.5698 (OUTLIER) cc_final: 0.5359 (t80) REVERT: A 472 MET cc_start: 0.7579 (tpt) cc_final: 0.7173 (tpt) REVERT: A 477 MET cc_start: 0.6804 (tpt) cc_final: 0.6381 (tpt) REVERT: A 526 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7637 (tt) REVERT: A 566 ILE cc_start: 0.7477 (tt) cc_final: 0.7209 (mt) REVERT: A 595 LYS cc_start: 0.7443 (mmmt) cc_final: 0.6996 (mmmt) REVERT: A 655 PHE cc_start: 0.5393 (OUTLIER) cc_final: 0.5070 (t80) REVERT: B 44 MET cc_start: 0.6839 (mtt) cc_final: 0.6078 (mtm) REVERT: B 84 ASP cc_start: 0.6353 (p0) cc_final: 0.5698 (p0) REVERT: B 113 GLU cc_start: 0.6430 (tt0) cc_final: 0.5973 (tt0) REVERT: B 166 ASN cc_start: 0.8241 (m-40) cc_final: 0.7420 (t0) REVERT: B 194 LYS cc_start: 0.7096 (mptp) cc_final: 0.6632 (mptp) REVERT: B 219 ILE cc_start: 0.7524 (tp) cc_final: 0.7187 (tp) REVERT: B 220 GLU cc_start: 0.6205 (tm-30) cc_final: 0.5946 (tm-30) REVERT: B 338 ARG cc_start: 0.7476 (ttp-170) cc_final: 0.7188 (ttp80) REVERT: B 440 CYS cc_start: 0.7923 (p) cc_final: 0.7679 (p) REVERT: B 464 MET cc_start: 0.4211 (ppp) cc_final: 0.3958 (ppp) REVERT: B 468 TYR cc_start: 0.6493 (m-10) cc_final: 0.5959 (m-10) REVERT: B 469 MET cc_start: 0.6843 (mmm) cc_final: 0.6507 (mmm) REVERT: B 481 ILE cc_start: 0.6911 (pt) cc_final: 0.6641 (tp) REVERT: B 492 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7935 (mmmt) REVERT: B 531 ILE cc_start: 0.7671 (tp) cc_final: 0.7410 (mt) REVERT: B 535 MET cc_start: 0.7165 (tpp) cc_final: 0.6914 (tpp) REVERT: B 572 TRP cc_start: 0.8019 (m-10) cc_final: 0.7663 (m100) REVERT: B 579 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.7723 (p) REVERT: B 597 TYR cc_start: 0.7419 (t80) cc_final: 0.6885 (t80) REVERT: B 622 MET cc_start: 0.6594 (mmm) cc_final: 0.5990 (mmm) outliers start: 55 outliers final: 46 residues processed: 246 average time/residue: 0.0816 time to fit residues: 27.6997 Evaluate side-chains 259 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 TRP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 683 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 83 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 500 HIS ** 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 = 0.4380 r_free = 0.4380 target = 0.192072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155387 restraints weight = 15602.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160069 restraints weight = 9336.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162787 restraints weight = 6511.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165182 restraints weight = 5169.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165990 restraints weight = 4368.887| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9775 Z= 0.160 Angle : 0.701 15.350 13269 Z= 0.355 Chirality : 0.044 0.216 1548 Planarity : 0.004 0.050 1632 Dihedral : 8.087 59.773 1509 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.05 % Allowed : 21.26 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.24), residues: 1182 helix: 1.15 (0.22), residues: 521 sheet: -1.09 (0.56), residues: 87 loop : -1.53 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.020 0.002 TYR A 691 PHE 0.023 0.001 PHE A 102 TRP 0.030 0.002 TRP A 561 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9756) covalent geometry : angle 0.68513 (13225) SS BOND : bond 0.00501 ( 13) SS BOND : angle 1.44535 ( 26) hydrogen bonds : bond 0.04511 ( 446) hydrogen bonds : angle 4.78442 ( 1305) link_NAG-ASN : bond 0.00308 ( 6) link_NAG-ASN : angle 3.73834 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 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: symmetry clash REVERT: A 70 MET cc_start: 0.6717 (ttm) cc_final: 0.6231 (ptt) REVERT: A 115 ASP cc_start: 0.6858 (p0) cc_final: 0.6529 (p0) REVERT: A 141 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7556 (mmpt) REVERT: A 151 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7842 (mmtm) REVERT: A 177 MET cc_start: 0.8208 (tpp) cc_final: 0.7231 (mmm) REVERT: A 189 ASP cc_start: 0.6923 (t0) cc_final: 0.6443 (t0) REVERT: A 224 TYR cc_start: 0.7219 (m-80) cc_final: 0.6712 (m-80) REVERT: A 252 ASN cc_start: 0.7496 (t0) cc_final: 0.7258 (t0) REVERT: A 290 SER cc_start: 0.8420 (t) cc_final: 0.7958 (p) REVERT: A 477 MET cc_start: 0.6794 (tpt) cc_final: 0.6342 (tpt) REVERT: A 526 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7670 (tt) REVERT: A 566 ILE cc_start: 0.7475 (tt) cc_final: 0.7033 (mt) REVERT: A 570 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7825 (mm) REVERT: A 595 LYS cc_start: 0.7425 (mmmt) cc_final: 0.6981 (mmmt) REVERT: A 646 ASP cc_start: 0.6247 (m-30) cc_final: 0.5598 (p0) REVERT: A 655 PHE cc_start: 0.5877 (OUTLIER) cc_final: 0.5532 (t80) REVERT: B 44 MET cc_start: 0.6757 (mtt) cc_final: 0.6017 (mtm) REVERT: B 84 ASP cc_start: 0.6373 (p0) cc_final: 0.5749 (p0) REVERT: B 113 GLU cc_start: 0.6445 (tt0) cc_final: 0.5934 (tt0) REVERT: B 166 ASN cc_start: 0.8235 (m-40) cc_final: 0.7419 (t0) REVERT: B 194 LYS cc_start: 0.7041 (mptp) cc_final: 0.6585 (mptp) REVERT: B 215 GLU cc_start: 0.7075 (mp0) cc_final: 0.6708 (mp0) REVERT: B 219 ILE cc_start: 0.7499 (tp) cc_final: 0.7153 (tp) REVERT: B 220 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5939 (tm-30) REVERT: B 338 ARG cc_start: 0.7472 (ttp-170) cc_final: 0.7186 (ttp80) REVERT: B 440 CYS cc_start: 0.7918 (p) cc_final: 0.7681 (p) REVERT: B 464 MET cc_start: 0.4222 (ppp) cc_final: 0.3956 (ppp) REVERT: B 468 TYR cc_start: 0.6521 (m-10) cc_final: 0.6055 (m-10) REVERT: B 469 MET cc_start: 0.6846 (mmm) cc_final: 0.6366 (mmm) REVERT: B 477 MET cc_start: 0.7003 (tpt) cc_final: 0.6655 (tpt) REVERT: B 481 ILE cc_start: 0.6883 (pt) cc_final: 0.6632 (tp) REVERT: B 492 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7815 (mmmt) REVERT: B 499 ARG cc_start: 0.7183 (mpp80) cc_final: 0.6976 (mpp80) REVERT: B 531 ILE cc_start: 0.7678 (tp) cc_final: 0.7424 (mt) REVERT: B 535 MET cc_start: 0.7173 (tpp) cc_final: 0.6942 (tpp) REVERT: B 572 TRP cc_start: 0.8006 (m-10) cc_final: 0.7665 (m100) REVERT: B 597 TYR cc_start: 0.7345 (t80) cc_final: 0.6737 (t80) REVERT: B 622 MET cc_start: 0.6647 (mmm) cc_final: 0.6037 (mmm) outliers start: 53 outliers final: 43 residues processed: 241 average time/residue: 0.0925 time to fit residues: 30.6922 Evaluate side-chains 248 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 572 TRP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 683 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.188750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151946 restraints weight = 15632.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.156203 restraints weight = 9659.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159158 restraints weight = 6930.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.161108 restraints weight = 5491.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.162439 restraints weight = 4729.542| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9775 Z= 0.231 Angle : 0.762 15.996 13269 Z= 0.388 Chirality : 0.046 0.219 1548 Planarity : 0.005 0.051 1632 Dihedral : 8.027 58.287 1506 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.86 % Allowed : 21.93 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.24), residues: 1182 helix: 0.88 (0.22), residues: 527 sheet: -1.22 (0.56), residues: 87 loop : -1.66 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.017 0.002 TYR A 498 PHE 0.021 0.002 PHE A 102 TRP 0.038 0.002 TRP A 561 HIS 0.009 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9756) covalent geometry : angle 0.74197 (13225) SS BOND : bond 0.00581 ( 13) SS BOND : angle 2.52950 ( 26) hydrogen bonds : bond 0.04942 ( 446) hydrogen bonds : angle 4.96552 ( 1305) link_NAG-ASN : bond 0.00250 ( 6) link_NAG-ASN : angle 3.82965 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6847 (ttm) cc_final: 0.6352 (ptt) REVERT: A 115 ASP cc_start: 0.6861 (p0) cc_final: 0.6499 (p0) REVERT: A 141 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7532 (mmpt) REVERT: A 151 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7816 (mmtm) REVERT: A 177 MET cc_start: 0.8209 (tpp) cc_final: 0.7536 (mmm) REVERT: A 189 ASP cc_start: 0.6954 (t0) cc_final: 0.6482 (t0) REVERT: A 224 TYR cc_start: 0.7510 (m-80) cc_final: 0.7037 (m-80) REVERT: A 252 ASN cc_start: 0.7585 (t0) cc_final: 0.7307 (t0) REVERT: A 290 SER cc_start: 0.8450 (t) cc_final: 0.8009 (p) REVERT: A 472 MET cc_start: 0.7682 (tpt) cc_final: 0.7325 (tpt) REVERT: A 477 MET cc_start: 0.6799 (tpt) cc_final: 0.6376 (tpt) REVERT: A 488 ILE cc_start: 0.7956 (pt) cc_final: 0.7688 (pt) REVERT: A 526 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7602 (tt) REVERT: A 566 ILE cc_start: 0.7508 (tt) cc_final: 0.7248 (mt) REVERT: A 595 LYS cc_start: 0.7457 (mmmt) cc_final: 0.7014 (mmmt) REVERT: A 646 ASP cc_start: 0.6302 (m-30) cc_final: 0.5676 (p0) REVERT: A 655 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5672 (t80) REVERT: B 44 MET cc_start: 0.6776 (mtt) cc_final: 0.6032 (mtm) REVERT: B 84 ASP cc_start: 0.6396 (p0) cc_final: 0.5756 (p0) REVERT: B 113 GLU cc_start: 0.6494 (tt0) cc_final: 0.5983 (tt0) REVERT: B 166 ASN cc_start: 0.8305 (m-40) cc_final: 0.7489 (t0) REVERT: B 194 LYS cc_start: 0.6921 (mptp) cc_final: 0.6496 (mptp) REVERT: B 207 LYS cc_start: 0.7959 (mmmm) cc_final: 0.7472 (mmmm) REVERT: B 219 ILE cc_start: 0.7538 (tp) cc_final: 0.7171 (tp) REVERT: B 239 ASN cc_start: 0.7750 (p0) cc_final: 0.7545 (p0) REVERT: B 338 ARG cc_start: 0.7489 (ttp-170) cc_final: 0.7222 (ttp80) REVERT: B 440 CYS cc_start: 0.7899 (p) cc_final: 0.7676 (p) REVERT: B 464 MET cc_start: 0.4202 (ppp) cc_final: 0.3954 (ppp) REVERT: B 468 TYR cc_start: 0.6488 (m-10) cc_final: 0.6015 (m-10) REVERT: B 469 MET cc_start: 0.6877 (mmm) cc_final: 0.6400 (mmm) REVERT: B 481 ILE cc_start: 0.6929 (pt) cc_final: 0.6664 (tp) REVERT: B 492 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7957 (mmmt) REVERT: B 531 ILE cc_start: 0.7712 (tp) cc_final: 0.7472 (mt) REVERT: B 558 ILE cc_start: 0.7653 (mm) cc_final: 0.7314 (pt) REVERT: B 572 TRP cc_start: 0.8048 (m-10) cc_final: 0.7726 (m100) REVERT: B 579 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.7743 (p) REVERT: B 597 TYR cc_start: 0.7450 (t80) cc_final: 0.6860 (t80) REVERT: B 622 MET cc_start: 0.6700 (mmm) cc_final: 0.6078 (mmm) outliers start: 51 outliers final: 45 residues processed: 246 average time/residue: 0.0933 time to fit residues: 31.2453 Evaluate side-chains 260 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 TRP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 683 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.191483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154649 restraints weight = 15575.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.159140 restraints weight = 9398.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162185 restraints weight = 6628.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.164311 restraints weight = 5203.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.165172 restraints weight = 4427.833| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9775 Z= 0.172 Angle : 0.729 16.502 13269 Z= 0.369 Chirality : 0.044 0.218 1548 Planarity : 0.004 0.050 1632 Dihedral : 7.746 57.949 1504 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.67 % Allowed : 22.21 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.24), residues: 1182 helix: 0.95 (0.22), residues: 526 sheet: -1.27 (0.51), residues: 105 loop : -1.51 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.017 0.001 TYR A 87 PHE 0.023 0.002 PHE A 102 TRP 0.028 0.002 TRP A 561 HIS 0.010 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9756) covalent geometry : angle 0.71089 (13225) SS BOND : bond 0.00555 ( 13) SS BOND : angle 2.09172 ( 26) hydrogen bonds : bond 0.04560 ( 446) hydrogen bonds : angle 4.85491 ( 1305) link_NAG-ASN : bond 0.00279 ( 6) link_NAG-ASN : angle 3.76696 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.34 seconds wall clock time: 26 minutes 0.97 seconds (1560.97 seconds total)