Starting phenix.real_space_refine on Tue Feb 3 20:07:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9krb_62525/02_2026/9krb_62525.cif Found real_map, /net/cci-nas-00/data/ceres_data/9krb_62525/02_2026/9krb_62525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9krb_62525/02_2026/9krb_62525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9krb_62525/02_2026/9krb_62525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9krb_62525/02_2026/9krb_62525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9krb_62525/02_2026/9krb_62525.map" } resolution = 3.22 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= 0.002 sd= 0.149 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 39 5.16 5 C 4191 2.51 5 N 1065 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s 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: 6587 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1545 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 13, 'TRANS': 185} Chain: "B" Number of atoms: 4888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4888 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 570} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.02, per 1000 atoms: 0.15 Number of scatterers: 6587 At special positions: 0 Unit cell: (80.438, 88.047, 125.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1292 8.00 N 1065 7.00 C 4191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 445 " - pdb=" SG CYS A 583 " distance=2.04 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 601 " - " ASN A 495 " " NAG C 1 " - " ASN A 418 " " NAG D 1 " - " ASN B 52 " " NAG E 1 " - " ASN B 78 " " NAG F 1 " - " ASN B 322 " " NAG G 1 " - " ASN B 546 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 143.8 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1506 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 46.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.984A pdb=" N THR A 398 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.578A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.914A pdb=" N SER A 461 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 removed outlier: 3.859A pdb=" N PHE A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'B' and resid 20 through 35 Processing helix chain 'B' and resid 37 through 51 removed outlier: 3.672A pdb=" N GLU B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.554A pdb=" N ASN B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 80 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.851A pdb=" N VAL B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 107' Processing helix chain 'B' and resid 110 through 128 removed outlier: 3.960A pdb=" N SER B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 removed outlier: 4.113A pdb=" N ILE B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.603A pdb=" N GLU B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 204 removed outlier: 3.532A pdb=" N TYR B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP B 202 " --> pdb=" O TYR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.785A pdb=" N LYS B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 242 through 252 removed outlier: 3.695A pdb=" N VAL B 250 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 314 through 319 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 371 through 383 removed outlier: 3.522A pdb=" N ILE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.569A pdb=" N ALA B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 404' Processing helix chain 'B' and resid 418 through 422 removed outlier: 3.605A pdb=" N LEU B 421 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 422 " --> pdb=" O LYS B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 422' Processing helix chain 'B' and resid 432 through 447 removed outlier: 4.193A pdb=" N ILE B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 removed outlier: 3.872A pdb=" N GLU B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.670A pdb=" N TRP B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.585A pdb=" N ALA B 502 " --> pdb=" O ASP B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 512 through 516 removed outlier: 3.748A pdb=" N TYR B 515 " --> pdb=" O PHE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 removed outlier: 3.632A pdb=" N GLN B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLN B 526 " --> pdb=" O GLN B 522 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 528 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.745A pdb=" N LYS B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 542' Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.614A pdb=" N PHE B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 409 removed outlier: 3.501A pdb=" N LYS A 408 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 448 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 417 removed outlier: 5.566A pdb=" N CYS A 415 " --> pdb=" O CYS A 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 431 through 434 Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.930A pdb=" N THR A 555 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS A 511 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 553 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 552 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.019A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 350 197 hydrogen bonds defined for protein. 564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.57 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1081 1.31 - 1.44: 1978 1.44 - 1.57: 3644 1.57 - 1.70: 0 1.70 - 1.83: 62 Bond restraints: 6765 Sorted by residual: bond pdb=" C ASP B 355 " pdb=" O ASP B 355 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.20e-02 6.94e+03 1.80e+01 bond pdb=" CA ASP B 355 " pdb=" C ASP B 355 " ideal model delta sigma weight residual 1.521 1.495 0.026 1.19e-02 7.06e+03 4.78e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.32e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.14e+00 ... (remaining 6760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 8742 1.66 - 3.32: 389 3.32 - 4.98: 40 4.98 - 6.63: 19 6.63 - 8.29: 10 Bond angle restraints: 9200 Sorted by residual: angle pdb=" N ASN B 354 " pdb=" CA ASN B 354 " pdb=" C ASN B 354 " ideal model delta sigma weight residual 113.56 121.08 -7.52 1.39e+00 5.18e-01 2.93e+01 angle pdb=" N VAL B 506 " pdb=" CA VAL B 506 " pdb=" C VAL B 506 " ideal model delta sigma weight residual 111.81 108.06 3.75 8.60e-01 1.35e+00 1.90e+01 angle pdb=" C ASP B 19 " pdb=" N ILE B 20 " pdb=" CA ILE B 20 " ideal model delta sigma weight residual 121.97 129.28 -7.31 1.80e+00 3.09e-01 1.65e+01 angle pdb=" C ASN B 354 " pdb=" N ASP B 355 " pdb=" CA ASP B 355 " ideal model delta sigma weight residual 122.99 117.42 5.57 1.41e+00 5.03e-01 1.56e+01 angle pdb=" N ILE B 232 " pdb=" CA ILE B 232 " pdb=" C ILE B 232 " ideal model delta sigma weight residual 112.80 108.30 4.50 1.15e+00 7.56e-01 1.53e+01 ... (remaining 9195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3721 17.85 - 35.70: 302 35.70 - 53.54: 97 53.54 - 71.39: 21 71.39 - 89.24: 14 Dihedral angle restraints: 4155 sinusoidal: 1805 harmonic: 2350 Sorted by residual: dihedral pdb=" CA PHE B 210 " pdb=" C PHE B 210 " pdb=" N PRO B 211 " pdb=" CA PRO B 211 " ideal model delta harmonic sigma weight residual -180.00 -116.11 -63.89 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA LYS B 233 " pdb=" C LYS B 233 " pdb=" N PRO B 234 " pdb=" CA PRO B 234 " ideal model delta harmonic sigma weight residual 180.00 137.13 42.87 0 5.00e+00 4.00e-02 7.35e+01 dihedral pdb=" CA ASP B 148 " pdb=" C ASP B 148 " pdb=" N ALA B 149 " pdb=" CA ALA B 149 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 4152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 824 0.066 - 0.132: 168 0.132 - 0.198: 15 0.198 - 0.264: 1 0.264 - 0.330: 2 Chirality restraints: 1010 Sorted by residual: chirality pdb=" CA ASN B 354 " pdb=" N ASN B 354 " pdb=" C ASN B 354 " pdb=" CB ASN B 354 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA ASP B 355 " pdb=" N ASP B 355 " pdb=" C ASP B 355 " pdb=" CB ASP B 355 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO B 211 " pdb=" N PRO B 211 " pdb=" C PRO B 211 " pdb=" CB PRO B 211 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1007 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 233 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO B 234 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 210 " 0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 211 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 450 " -0.041 5.00e-02 4.00e+02 6.03e-02 5.83e+00 pdb=" N PRO B 451 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " -0.034 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2165 2.83 - 3.35: 5226 3.35 - 3.87: 10380 3.87 - 4.38: 12249 4.38 - 4.90: 21821 Nonbonded interactions: 51841 Sorted by model distance: nonbonded pdb=" OH TYR A 417 " pdb=" O GLY A 444 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR B 182 " pdb=" OD1 ASP B 509 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR A 456 " pdb=" O MET A 460 " model vdw 2.321 3.040 nonbonded pdb=" O PHE B 327 " pdb=" OG SER B 331 " model vdw 2.326 3.040 nonbonded pdb=" O ASP B 367 " pdb=" OG1 THR B 371 " model vdw 2.340 3.040 ... (remaining 51836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 5.230 Find NCS groups from input model: 0.020 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:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 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 : 0.007 0.063 6783 Z= 0.309 Angle : 0.848 10.701 9247 Z= 0.467 Chirality : 0.054 0.330 1010 Planarity : 0.008 0.116 1168 Dihedral : 15.710 89.240 2628 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.95 % Favored : 91.79 % Rotamer: Outliers : 7.15 % Allowed : 10.01 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % 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: -5.20 (0.21), residues: 792 helix: -3.63 (0.17), residues: 364 sheet: -3.57 (0.50), residues: 64 loop : -3.12 (0.25), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 476 TYR 0.023 0.002 TYR B 385 PHE 0.014 0.002 PHE B 327 TRP 0.010 0.002 TRP B 302 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 6765) covalent geometry : angle 0.82814 ( 9200) SS BOND : bond 0.00482 ( 7) SS BOND : angle 1.09121 ( 14) hydrogen bonds : bond 0.20911 ( 197) hydrogen bonds : angle 7.20591 ( 564) link_BETA1-4 : bond 0.00764 ( 5) link_BETA1-4 : angle 3.47428 ( 15) link_NAG-ASN : bond 0.00557 ( 6) link_NAG-ASN : angle 2.87317 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 0.168 Fit side-chains REVERT: A 478 LYS cc_start: 0.8642 (tttt) cc_final: 0.8029 (tttm) REVERT: A 501 LYS cc_start: 0.8216 (ttmt) cc_final: 0.8015 (ttmm) REVERT: B 97 GLN cc_start: 0.7410 (mt0) cc_final: 0.7046 (mt0) REVERT: B 170 ASP cc_start: 0.6719 (m-30) cc_final: 0.6317 (m-30) REVERT: B 259 THR cc_start: 0.8309 (p) cc_final: 0.7742 (t) REVERT: B 273 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7485 (ttt90) REVERT: B 287 ASN cc_start: 0.8135 (m-40) cc_final: 0.7891 (m110) REVERT: B 341 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7564 (ttpp) REVERT: B 394 SER cc_start: 0.8385 (t) cc_final: 0.8041 (m) REVERT: B 408 MET cc_start: 0.8063 (mmt) cc_final: 0.7585 (mmt) REVERT: B 460 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7693 (mtm180) REVERT: B 462 MET cc_start: 0.7779 (mtm) cc_final: 0.7437 (mtp) REVERT: B 475 LYS cc_start: 0.7793 (ttpp) cc_final: 0.7557 (tttp) REVERT: B 531 LYS cc_start: 0.7430 (ttmt) cc_final: 0.7186 (tttp) outliers start: 50 outliers final: 18 residues processed: 156 average time/residue: 0.0662 time to fit residues: 13.7432 Evaluate side-chains 103 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 527 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 HIS A 494 GLN B 23 GLN B 50 ASN B 220 GLN B 522 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.105593 restraints weight = 8103.795| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.17 r_work: 0.2790 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6783 Z= 0.123 Angle : 0.633 7.293 9247 Z= 0.323 Chirality : 0.043 0.243 1010 Planarity : 0.006 0.093 1168 Dihedral : 8.916 60.737 1151 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.32 % Favored : 92.55 % Rotamer: Outliers : 2.15 % Allowed : 15.02 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % 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: -4.08 (0.25), residues: 792 helix: -2.54 (0.23), residues: 364 sheet: -2.88 (0.52), residues: 68 loop : -2.77 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 340 TYR 0.013 0.001 TYR B 385 PHE 0.011 0.001 PHE B 210 TRP 0.009 0.001 TRP B 164 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6765) covalent geometry : angle 0.61398 ( 9200) SS BOND : bond 0.00594 ( 7) SS BOND : angle 1.69041 ( 14) hydrogen bonds : bond 0.04332 ( 197) hydrogen bonds : angle 5.09693 ( 564) link_BETA1-4 : bond 0.00409 ( 5) link_BETA1-4 : angle 2.20427 ( 15) link_NAG-ASN : bond 0.00271 ( 6) link_NAG-ASN : angle 2.57734 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.150 Fit side-chains REVERT: A 478 LYS cc_start: 0.8652 (tttt) cc_final: 0.8187 (tttp) REVERT: A 501 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8116 (ttmm) REVERT: B 170 ASP cc_start: 0.6948 (m-30) cc_final: 0.6567 (m-30) REVERT: B 259 THR cc_start: 0.8360 (p) cc_final: 0.7849 (t) REVERT: B 287 ASN cc_start: 0.8371 (m-40) cc_final: 0.8008 (m-40) REVERT: B 303 ASP cc_start: 0.8248 (t0) cc_final: 0.8018 (t0) REVERT: B 341 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7934 (ttpp) REVERT: B 394 SER cc_start: 0.8942 (t) cc_final: 0.8737 (m) REVERT: B 455 MET cc_start: 0.8799 (tmm) cc_final: 0.8007 (tmm) REVERT: B 460 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8475 (mtm180) REVERT: B 475 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8071 (tttp) REVERT: B 531 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7796 (tttp) outliers start: 15 outliers final: 8 residues processed: 101 average time/residue: 0.0776 time to fit residues: 10.2887 Evaluate side-chains 91 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 527 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.091231 restraints weight = 8267.722| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.28 r_work: 0.2756 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6783 Z= 0.170 Angle : 0.633 10.106 9247 Z= 0.318 Chirality : 0.044 0.237 1010 Planarity : 0.005 0.089 1168 Dihedral : 7.813 58.433 1126 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.17 % Rotamer: Outliers : 2.58 % Allowed : 16.17 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.26), residues: 792 helix: -1.98 (0.26), residues: 363 sheet: -2.67 (0.54), residues: 68 loop : -2.55 (0.28), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 460 TYR 0.014 0.001 TYR B 385 PHE 0.012 0.001 PHE B 210 TRP 0.008 0.001 TRP B 164 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 6765) covalent geometry : angle 0.61163 ( 9200) SS BOND : bond 0.00911 ( 7) SS BOND : angle 2.00987 ( 14) hydrogen bonds : bond 0.04164 ( 197) hydrogen bonds : angle 4.82555 ( 564) link_BETA1-4 : bond 0.00361 ( 5) link_BETA1-4 : angle 2.09313 ( 15) link_NAG-ASN : bond 0.00524 ( 6) link_NAG-ASN : angle 2.83566 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.154 Fit side-chains REVERT: A 478 LYS cc_start: 0.8637 (tttt) cc_final: 0.8160 (tttp) REVERT: A 501 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8102 (ttmm) REVERT: B 170 ASP cc_start: 0.6971 (m-30) cc_final: 0.6509 (m-30) REVERT: B 259 THR cc_start: 0.8370 (p) cc_final: 0.7868 (t) REVERT: B 273 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8120 (ttt90) REVERT: B 287 ASN cc_start: 0.8427 (m-40) cc_final: 0.8062 (m-40) REVERT: B 303 ASP cc_start: 0.8262 (t0) cc_final: 0.7989 (t0) REVERT: B 341 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7887 (ttpp) REVERT: B 394 SER cc_start: 0.8944 (t) cc_final: 0.8725 (m) REVERT: B 455 MET cc_start: 0.8860 (tmm) cc_final: 0.8018 (tmm) REVERT: B 460 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8393 (mtm180) REVERT: B 462 MET cc_start: 0.8714 (mtp) cc_final: 0.8438 (mtp) REVERT: B 475 LYS cc_start: 0.8365 (ttpp) cc_final: 0.8020 (tttp) REVERT: B 531 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7752 (tttp) outliers start: 18 outliers final: 10 residues processed: 96 average time/residue: 0.0675 time to fit residues: 8.5401 Evaluate side-chains 90 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 527 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.0570 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105263 restraints weight = 8084.776| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.15 r_work: 0.2823 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6783 Z= 0.103 Angle : 0.571 6.409 9247 Z= 0.285 Chirality : 0.042 0.257 1010 Planarity : 0.005 0.084 1168 Dihedral : 7.164 56.135 1124 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.56 % Rotamer: Outliers : 2.72 % Allowed : 16.17 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % 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: -2.99 (0.28), residues: 792 helix: -1.58 (0.27), residues: 362 sheet: -2.25 (0.59), residues: 68 loop : -2.27 (0.28), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 460 TYR 0.009 0.001 TYR B 497 PHE 0.010 0.001 PHE B 210 TRP 0.006 0.001 TRP B 164 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6765) covalent geometry : angle 0.55127 ( 9200) SS BOND : bond 0.00563 ( 7) SS BOND : angle 1.23986 ( 14) hydrogen bonds : bond 0.03311 ( 197) hydrogen bonds : angle 4.58028 ( 564) link_BETA1-4 : bond 0.00438 ( 5) link_BETA1-4 : angle 1.89810 ( 15) link_NAG-ASN : bond 0.00363 ( 6) link_NAG-ASN : angle 2.82975 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.189 Fit side-chains REVERT: A 478 LYS cc_start: 0.8735 (tttt) cc_final: 0.8283 (tttp) REVERT: A 566 GLN cc_start: 0.7837 (mt0) cc_final: 0.7248 (mt0) REVERT: B 170 ASP cc_start: 0.7139 (m-30) cc_final: 0.6630 (m-30) REVERT: B 259 THR cc_start: 0.8455 (p) cc_final: 0.7958 (t) REVERT: B 273 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8374 (ttt180) REVERT: B 287 ASN cc_start: 0.8491 (m-40) cc_final: 0.8147 (m-40) REVERT: B 303 ASP cc_start: 0.8237 (t0) cc_final: 0.8003 (t0) REVERT: B 341 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7812 (ttpp) REVERT: B 347 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8671 (p) REVERT: B 430 GLU cc_start: 0.6840 (tp30) cc_final: 0.6537 (tp30) REVERT: B 455 MET cc_start: 0.8870 (tmm) cc_final: 0.8033 (tmm) REVERT: B 460 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8441 (mtm180) REVERT: B 462 MET cc_start: 0.8829 (mtp) cc_final: 0.8534 (mtp) REVERT: B 475 LYS cc_start: 0.8472 (ttpp) cc_final: 0.8149 (tttp) outliers start: 19 outliers final: 7 residues processed: 104 average time/residue: 0.0701 time to fit residues: 9.6256 Evaluate side-chains 88 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 600 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 0.0060 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.137122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103787 restraints weight = 8245.311| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.16 r_work: 0.2778 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6783 Z= 0.188 Angle : 0.628 10.011 9247 Z= 0.312 Chirality : 0.045 0.298 1010 Planarity : 0.006 0.116 1168 Dihedral : 6.638 56.951 1117 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.83 % Favored : 92.05 % Rotamer: Outliers : 3.00 % Allowed : 16.31 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % 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: -2.83 (0.28), residues: 792 helix: -1.43 (0.28), residues: 363 sheet: -2.12 (0.60), residues: 68 loop : -2.23 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 393 TYR 0.015 0.001 TYR B 385 PHE 0.012 0.001 PHE B 327 TRP 0.008 0.001 TRP B 478 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 6765) covalent geometry : angle 0.60222 ( 9200) SS BOND : bond 0.00470 ( 7) SS BOND : angle 1.10729 ( 14) hydrogen bonds : bond 0.04027 ( 197) hydrogen bonds : angle 4.61004 ( 564) link_BETA1-4 : bond 0.00389 ( 5) link_BETA1-4 : angle 1.97298 ( 15) link_NAG-ASN : bond 0.00404 ( 6) link_NAG-ASN : angle 3.58907 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.230 Fit side-chains REVERT: A 465 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8318 (mm-40) REVERT: A 478 LYS cc_start: 0.8790 (tttt) cc_final: 0.8320 (tttp) REVERT: A 566 GLN cc_start: 0.7809 (mt0) cc_final: 0.7228 (mt0) REVERT: B 170 ASP cc_start: 0.7110 (m-30) cc_final: 0.6649 (m-30) REVERT: B 259 THR cc_start: 0.8546 (p) cc_final: 0.8028 (t) REVERT: B 273 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8264 (ttt90) REVERT: B 287 ASN cc_start: 0.8505 (m-40) cc_final: 0.8157 (m-40) REVERT: B 303 ASP cc_start: 0.8342 (t0) cc_final: 0.8090 (t0) REVERT: B 341 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7810 (ttpp) REVERT: B 347 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8707 (p) REVERT: B 430 GLU cc_start: 0.6843 (tp30) cc_final: 0.6540 (tp30) REVERT: B 455 MET cc_start: 0.8918 (tmm) cc_final: 0.8061 (tmm) REVERT: B 460 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8607 (mtm180) REVERT: B 475 LYS cc_start: 0.8468 (ttpp) cc_final: 0.8141 (tttp) outliers start: 21 outliers final: 14 residues processed: 100 average time/residue: 0.0687 time to fit residues: 9.2272 Evaluate side-chains 100 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 600 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106667 restraints weight = 8162.242| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.12 r_work: 0.2818 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6783 Z= 0.117 Angle : 0.592 10.372 9247 Z= 0.291 Chirality : 0.043 0.281 1010 Planarity : 0.005 0.107 1168 Dihedral : 6.541 55.055 1117 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.69 % Favored : 93.18 % Rotamer: Outliers : 2.29 % Allowed : 17.45 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % 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: -2.53 (0.29), residues: 792 helix: -1.23 (0.28), residues: 365 sheet: -1.89 (0.60), residues: 68 loop : -2.02 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 518 TYR 0.010 0.001 TYR B 497 PHE 0.009 0.001 PHE B 327 TRP 0.006 0.001 TRP B 164 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6765) covalent geometry : angle 0.56181 ( 9200) SS BOND : bond 0.00639 ( 7) SS BOND : angle 1.19340 ( 14) hydrogen bonds : bond 0.03312 ( 197) hydrogen bonds : angle 4.51348 ( 564) link_BETA1-4 : bond 0.00421 ( 5) link_BETA1-4 : angle 1.88718 ( 15) link_NAG-ASN : bond 0.00423 ( 6) link_NAG-ASN : angle 3.79309 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.189 Fit side-chains REVERT: A 478 LYS cc_start: 0.8766 (tttt) cc_final: 0.8325 (tttm) REVERT: A 566 GLN cc_start: 0.7798 (mt0) cc_final: 0.7217 (mt0) REVERT: B 170 ASP cc_start: 0.7130 (m-30) cc_final: 0.6654 (m-30) REVERT: B 259 THR cc_start: 0.8529 (p) cc_final: 0.8009 (t) REVERT: B 273 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8402 (ttt180) REVERT: B 287 ASN cc_start: 0.8520 (m-40) cc_final: 0.8174 (m-40) REVERT: B 303 ASP cc_start: 0.8269 (t0) cc_final: 0.8047 (t0) REVERT: B 316 ILE cc_start: 0.8644 (tp) cc_final: 0.8434 (pt) REVERT: B 323 MET cc_start: 0.8649 (mmt) cc_final: 0.8149 (mmt) REVERT: B 347 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8685 (p) REVERT: B 430 GLU cc_start: 0.6831 (tp30) cc_final: 0.6523 (tp30) REVERT: B 455 MET cc_start: 0.8889 (tmm) cc_final: 0.8022 (tmm) REVERT: B 460 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8505 (mtm180) REVERT: B 462 MET cc_start: 0.8862 (mtp) cc_final: 0.8603 (mtp) REVERT: B 475 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8124 (tttp) REVERT: B 531 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7726 (tttp) outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 0.0773 time to fit residues: 9.7382 Evaluate side-chains 97 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 600 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.137258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103621 restraints weight = 8207.040| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.15 r_work: 0.2781 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6783 Z= 0.183 Angle : 0.625 12.245 9247 Z= 0.307 Chirality : 0.045 0.311 1010 Planarity : 0.006 0.122 1168 Dihedral : 6.492 55.188 1113 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.17 % Rotamer: Outliers : 2.72 % Allowed : 17.02 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % 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: -2.48 (0.29), residues: 792 helix: -1.24 (0.28), residues: 368 sheet: -1.73 (0.62), residues: 66 loop : -1.97 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 460 TYR 0.014 0.001 TYR B 385 PHE 0.013 0.001 PHE B 327 TRP 0.006 0.001 TRP B 478 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6765) covalent geometry : angle 0.59403 ( 9200) SS BOND : bond 0.00610 ( 7) SS BOND : angle 1.34270 ( 14) hydrogen bonds : bond 0.03822 ( 197) hydrogen bonds : angle 4.55756 ( 564) link_BETA1-4 : bond 0.00376 ( 5) link_BETA1-4 : angle 1.94500 ( 15) link_NAG-ASN : bond 0.00774 ( 6) link_NAG-ASN : angle 3.98892 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.253 Fit side-chains REVERT: A 465 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8342 (mm-40) REVERT: A 478 LYS cc_start: 0.8789 (tttt) cc_final: 0.8319 (tttp) REVERT: A 566 GLN cc_start: 0.7791 (mt0) cc_final: 0.7221 (mt0) REVERT: B 170 ASP cc_start: 0.7103 (m-30) cc_final: 0.6646 (m-30) REVERT: B 259 THR cc_start: 0.8550 (p) cc_final: 0.8042 (t) REVERT: B 273 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8299 (ttt90) REVERT: B 287 ASN cc_start: 0.8509 (m-40) cc_final: 0.8159 (m-40) REVERT: B 303 ASP cc_start: 0.8283 (t0) cc_final: 0.8050 (t0) REVERT: B 323 MET cc_start: 0.8468 (mmt) cc_final: 0.7827 (mmt) REVERT: B 347 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8704 (p) REVERT: B 430 GLU cc_start: 0.6874 (tp30) cc_final: 0.6629 (tp30) REVERT: B 455 MET cc_start: 0.8915 (tmm) cc_final: 0.8056 (tmm) REVERT: B 460 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8591 (mtm180) REVERT: B 462 MET cc_start: 0.8872 (mtp) cc_final: 0.8598 (mtp) REVERT: B 475 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8145 (tttp) REVERT: B 531 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7823 (tttp) outliers start: 19 outliers final: 13 residues processed: 95 average time/residue: 0.0743 time to fit residues: 9.4858 Evaluate side-chains 95 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 600 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.0370 chunk 16 optimal weight: 7.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106513 restraints weight = 8175.906| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.16 r_work: 0.2808 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6783 Z= 0.100 Angle : 0.569 8.426 9247 Z= 0.279 Chirality : 0.042 0.261 1010 Planarity : 0.005 0.114 1168 Dihedral : 6.261 53.688 1113 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.56 % Rotamer: Outliers : 2.29 % Allowed : 17.60 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % 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: -2.21 (0.29), residues: 792 helix: -1.03 (0.28), residues: 368 sheet: -1.53 (0.63), residues: 66 loop : -1.84 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 518 TYR 0.009 0.001 TYR A 507 PHE 0.009 0.001 PHE B 327 TRP 0.006 0.001 TRP B 349 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6765) covalent geometry : angle 0.54490 ( 9200) SS BOND : bond 0.00496 ( 7) SS BOND : angle 1.00645 ( 14) hydrogen bonds : bond 0.03129 ( 197) hydrogen bonds : angle 4.42836 ( 564) link_BETA1-4 : bond 0.00485 ( 5) link_BETA1-4 : angle 1.85407 ( 15) link_NAG-ASN : bond 0.00546 ( 6) link_NAG-ASN : angle 3.28090 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8653 (tttt) cc_final: 0.8186 (tttm) REVERT: A 566 GLN cc_start: 0.7689 (mt0) cc_final: 0.7106 (mt0) REVERT: B 170 ASP cc_start: 0.7036 (m-30) cc_final: 0.6481 (m-30) REVERT: B 259 THR cc_start: 0.8476 (p) cc_final: 0.7958 (t) REVERT: B 273 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8326 (ttt180) REVERT: B 287 ASN cc_start: 0.8547 (m-40) cc_final: 0.8196 (m-40) REVERT: B 303 ASP cc_start: 0.8261 (t0) cc_final: 0.8003 (t0) REVERT: B 347 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8592 (p) REVERT: B 430 GLU cc_start: 0.6934 (tp30) cc_final: 0.6702 (tp30) REVERT: B 455 MET cc_start: 0.8839 (tmm) cc_final: 0.7982 (tmm) REVERT: B 460 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8317 (mtm180) REVERT: B 462 MET cc_start: 0.8788 (mtp) cc_final: 0.8515 (mtp) REVERT: B 475 LYS cc_start: 0.8349 (ttpp) cc_final: 0.8014 (tttp) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.0802 time to fit residues: 10.4431 Evaluate side-chains 96 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 600 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107229 restraints weight = 8218.053| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.15 r_work: 0.2818 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6783 Z= 0.101 Angle : 0.559 7.880 9247 Z= 0.273 Chirality : 0.041 0.227 1010 Planarity : 0.005 0.123 1168 Dihedral : 6.084 53.484 1113 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.69 % Favored : 93.18 % Rotamer: Outliers : 2.43 % Allowed : 17.60 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.30), residues: 792 helix: -0.81 (0.29), residues: 365 sheet: -1.31 (0.63), residues: 66 loop : -1.73 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 460 TYR 0.009 0.001 TYR A 507 PHE 0.010 0.001 PHE B 327 TRP 0.006 0.001 TRP B 164 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6765) covalent geometry : angle 0.53749 ( 9200) SS BOND : bond 0.00453 ( 7) SS BOND : angle 0.97315 ( 14) hydrogen bonds : bond 0.03061 ( 197) hydrogen bonds : angle 4.31056 ( 564) link_BETA1-4 : bond 0.00434 ( 5) link_BETA1-4 : angle 1.77883 ( 15) link_NAG-ASN : bond 0.00663 ( 6) link_NAG-ASN : angle 3.11284 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8622 (tttt) cc_final: 0.8140 (tttm) REVERT: A 566 GLN cc_start: 0.7689 (mt0) cc_final: 0.7125 (mt0) REVERT: B 59 LYS cc_start: 0.8108 (tppt) cc_final: 0.7565 (tmtt) REVERT: B 170 ASP cc_start: 0.6973 (m-30) cc_final: 0.6458 (m-30) REVERT: B 259 THR cc_start: 0.8466 (p) cc_final: 0.7962 (t) REVERT: B 273 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8318 (ttt180) REVERT: B 287 ASN cc_start: 0.8560 (m-40) cc_final: 0.8188 (m-40) REVERT: B 347 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8604 (p) REVERT: B 430 GLU cc_start: 0.6904 (tp30) cc_final: 0.6683 (tp30) REVERT: B 455 MET cc_start: 0.8834 (tmm) cc_final: 0.7990 (tmm) REVERT: B 460 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8279 (mtm180) REVERT: B 462 MET cc_start: 0.8777 (mtp) cc_final: 0.8497 (mtp) REVERT: B 475 LYS cc_start: 0.8345 (ttpp) cc_final: 0.8011 (tttp) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.0789 time to fit residues: 9.8354 Evaluate side-chains 92 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 600 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.0470 chunk 5 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108118 restraints weight = 8168.451| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.13 r_work: 0.2822 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6783 Z= 0.112 Angle : 0.617 16.778 9247 Z= 0.302 Chirality : 0.043 0.290 1010 Planarity : 0.005 0.127 1168 Dihedral : 6.113 53.602 1113 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.69 % Rotamer: Outliers : 2.29 % Allowed : 18.17 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.30), residues: 792 helix: -0.71 (0.28), residues: 371 sheet: -1.15 (0.63), residues: 67 loop : -1.71 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 487 TYR 0.009 0.001 TYR B 497 PHE 0.013 0.001 PHE B 315 TRP 0.006 0.001 TRP B 164 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6765) covalent geometry : angle 0.59157 ( 9200) SS BOND : bond 0.00892 ( 7) SS BOND : angle 2.26752 ( 14) hydrogen bonds : bond 0.03063 ( 197) hydrogen bonds : angle 4.43707 ( 564) link_BETA1-4 : bond 0.00423 ( 5) link_BETA1-4 : angle 1.76531 ( 15) link_NAG-ASN : bond 0.00595 ( 6) link_NAG-ASN : angle 3.19160 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 432 SER cc_start: 0.7935 (t) cc_final: 0.7147 (p) REVERT: A 478 LYS cc_start: 0.8707 (tttt) cc_final: 0.8244 (tttm) REVERT: A 566 GLN cc_start: 0.7769 (mt0) cc_final: 0.7221 (mt0) REVERT: B 170 ASP cc_start: 0.7063 (m-30) cc_final: 0.6547 (m-30) REVERT: B 259 THR cc_start: 0.8527 (p) cc_final: 0.8035 (t) REVERT: B 273 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8359 (ttt180) REVERT: B 287 ASN cc_start: 0.8556 (m-40) cc_final: 0.8193 (m-40) REVERT: B 347 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8651 (p) REVERT: B 430 GLU cc_start: 0.6879 (tp30) cc_final: 0.6665 (tp30) REVERT: B 455 MET cc_start: 0.8878 (tmm) cc_final: 0.8017 (tmm) REVERT: B 460 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8397 (mtm180) REVERT: B 462 MET cc_start: 0.8869 (mtp) cc_final: 0.8591 (mtp) REVERT: B 475 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8133 (tttp) REVERT: B 559 GLU cc_start: 0.8664 (tt0) cc_final: 0.8403 (pt0) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.0693 time to fit residues: 8.5268 Evaluate side-chains 97 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 600 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107762 restraints weight = 8123.690| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.15 r_work: 0.2824 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6783 Z= 0.111 Angle : 0.597 14.133 9247 Z= 0.292 Chirality : 0.042 0.236 1010 Planarity : 0.005 0.126 1168 Dihedral : 5.993 53.888 1113 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.06 % Favored : 93.81 % Rotamer: Outliers : 2.58 % Allowed : 18.17 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 5.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.30), residues: 792 helix: -0.56 (0.29), residues: 372 sheet: -1.08 (0.63), residues: 67 loop : -1.68 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 460 TYR 0.009 0.001 TYR B 497 PHE 0.010 0.001 PHE B 315 TRP 0.006 0.001 TRP B 349 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6765) covalent geometry : angle 0.57263 ( 9200) SS BOND : bond 0.00863 ( 7) SS BOND : angle 2.00305 ( 14) hydrogen bonds : bond 0.03096 ( 197) hydrogen bonds : angle 4.41225 ( 564) link_BETA1-4 : bond 0.00490 ( 5) link_BETA1-4 : angle 1.73974 ( 15) link_NAG-ASN : bond 0.00583 ( 6) link_NAG-ASN : angle 3.11391 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1473.43 seconds wall clock time: 25 minutes 49.30 seconds (1549.30 seconds total)