Starting phenix.real_space_refine on Tue Mar 3 15:21:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vx5_32169/03_2026/7vx5_32169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx5_32169/03_2026/7vx5_32169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vx5_32169/03_2026/7vx5_32169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx5_32169/03_2026/7vx5_32169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vx5_32169/03_2026/7vx5_32169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx5_32169/03_2026/7vx5_32169.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4144 2.51 5 N 1073 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6487 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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: 2.37, per 1000 atoms: 0.37 Number of scatterers: 6487 At special positions: 0 Unit cell: (77.603, 100.556, 118.044, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1232 8.00 N 1073 7.00 C 4144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 53 " " NAG E1301 " - " ASN E 343 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 338.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 57.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.644A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.682A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.524A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.903A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.610A pdb=" N LYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.527A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.767A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 4.010A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.588A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.754A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.905A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.649A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.647A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.912A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.561A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.106A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.504A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.471A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.583A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.038A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.604A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.821A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.575A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.880A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.849A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.592A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 389 removed outlier: 3.579A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 4.220A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.009A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.917A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.920A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 283 hydrogen bonds defined for protein. 797 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: 0.75 Time building geometry restraints manager: 0.85 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: 2080 1.34 - 1.46: 1694 1.46 - 1.58: 2836 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6668 Sorted by residual: bond pdb=" C LYS E 424 " pdb=" N LEU E 425 " ideal model delta sigma weight residual 1.331 1.374 -0.043 2.07e-02 2.33e+03 4.35e+00 bond pdb=" CA CYS E 336 " pdb=" C CYS E 336 " ideal model delta sigma weight residual 1.526 1.505 0.021 1.14e-02 7.69e+03 3.41e+00 bond pdb=" CA GLN E 484 " pdb=" C GLN E 484 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.38e-02 5.25e+03 2.57e+00 bond pdb=" C ALA A 36 " pdb=" N GLU A 37 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.31e-02 5.83e+03 2.35e+00 bond pdb=" CA VAL E 445 " pdb=" C VAL E 445 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.35e-02 5.49e+03 2.27e+00 ... (remaining 6663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 8677 1.49 - 2.99: 347 2.99 - 4.48: 34 4.48 - 5.97: 5 5.97 - 7.46: 1 Bond angle restraints: 9064 Sorted by residual: angle pdb=" N GLY E 446 " pdb=" CA GLY E 446 " pdb=" C GLY E 446 " ideal model delta sigma weight residual 115.36 107.90 7.46 1.33e+00 5.65e-01 3.15e+01 angle pdb=" N GLY A 147 " pdb=" CA GLY A 147 " pdb=" C GLY A 147 " ideal model delta sigma weight residual 112.64 117.74 -5.10 1.21e+00 6.83e-01 1.78e+01 angle pdb=" C VAL E 445 " pdb=" CA VAL E 445 " pdb=" CB VAL E 445 " ideal model delta sigma weight residual 111.32 105.41 5.91 1.63e+00 3.76e-01 1.31e+01 angle pdb=" C TYR E 495 " pdb=" N GLY E 496 " pdb=" CA GLY E 496 " ideal model delta sigma weight residual 120.98 117.78 3.20 9.00e-01 1.23e+00 1.27e+01 angle pdb=" C ALA A 36 " pdb=" N GLU A 37 " pdb=" CA GLU A 37 " ideal model delta sigma weight residual 120.28 116.09 4.19 1.34e+00 5.57e-01 9.78e+00 ... (remaining 9059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 3869 15.98 - 31.96: 89 31.96 - 47.95: 29 47.95 - 63.93: 10 63.93 - 79.91: 3 Dihedral angle restraints: 4000 sinusoidal: 1676 harmonic: 2324 Sorted by residual: dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N GLY A 147 " pdb=" CA GLY A 147 " ideal model delta harmonic sigma weight residual 180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA E 352 " pdb=" C ALA E 352 " pdb=" N TRP E 353 " pdb=" CA TRP E 353 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TYR A 497 " pdb=" C TYR A 497 " pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 760 0.050 - 0.100: 167 0.100 - 0.150: 30 0.150 - 0.200: 3 0.200 - 0.250: 1 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA VAL E 445 " pdb=" N VAL E 445 " pdb=" C VAL E 445 " pdb=" CB VAL E 445 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA GLN E 498 " pdb=" N GLN E 498 " pdb=" C GLN E 498 " pdb=" CB GLN E 498 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA GLU A 37 " pdb=" N GLU A 37 " pdb=" C GLU A 37 " pdb=" CB GLU A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 958 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 498 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO E 499 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 499 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 499 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 583 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 484 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C GLN E 484 " -0.025 2.00e-02 2.50e+03 pdb=" O GLN E 484 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY E 485 " 0.008 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1458 2.78 - 3.31: 6109 3.31 - 3.84: 10401 3.84 - 4.37: 12459 4.37 - 4.90: 21156 Nonbonded interactions: 51583 Sorted by model distance: nonbonded pdb=" OH TYR A 83 " pdb=" OD1 ASN E 487 " model vdw 2.246 3.040 nonbonded pdb=" N SER A 19 " pdb=" OE1 GLU A 23 " model vdw 2.264 3.120 nonbonded pdb=" O MET A 152 " pdb=" NH1 ARG A 161 " model vdw 2.270 3.120 nonbonded pdb=" OD1 ASN A 394 " pdb=" N GLY A 395 " model vdw 2.275 3.120 nonbonded pdb=" O MET A 190 " pdb=" ND2 ASN A 194 " model vdw 2.279 3.120 ... (remaining 51578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.950 Find NCS groups from input model: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 6682 Z= 0.181 Angle : 0.655 7.463 9093 Z= 0.422 Chirality : 0.044 0.250 961 Planarity : 0.004 0.065 1171 Dihedral : 9.062 79.909 2489 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.69 (0.25), residues: 788 helix: -2.96 (0.19), residues: 375 sheet: -0.42 (0.60), residues: 60 loop : -0.37 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.025 0.001 TYR E 495 PHE 0.020 0.002 PHE E 497 TRP 0.017 0.001 TRP A 302 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6668) covalent geometry : angle 0.65192 ( 9064) SS BOND : bond 0.00229 ( 7) SS BOND : angle 0.95133 ( 14) hydrogen bonds : bond 0.29514 ( 283) hydrogen bonds : angle 9.43504 ( 797) metal coordination : bond 0.06436 ( 2) link_NAG-ASN : bond 0.00148 ( 5) link_NAG-ASN : angle 1.44606 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8115 (p) cc_final: 0.7690 (t) REVERT: A 79 LEU cc_start: 0.8070 (mt) cc_final: 0.7867 (mp) REVERT: A 98 GLN cc_start: 0.8329 (tt0) cc_final: 0.7717 (mm110) REVERT: A 217 TYR cc_start: 0.8174 (t80) cc_final: 0.7328 (t80) REVERT: A 259 ILE cc_start: 0.8398 (pt) cc_final: 0.8148 (mp) REVERT: A 270 MET cc_start: 0.2479 (tpp) cc_final: 0.2262 (tpp) REVERT: A 323 MET cc_start: 0.7078 (mmp) cc_final: 0.5950 (mmt) REVERT: A 411 SER cc_start: 0.8513 (m) cc_final: 0.8295 (p) REVERT: A 513 ILE cc_start: 0.6925 (tp) cc_final: 0.6477 (tt) REVERT: A 531 GLN cc_start: 0.7367 (tt0) cc_final: 0.7059 (tp40) REVERT: E 356 LYS cc_start: 0.8394 (tttp) cc_final: 0.8133 (ttmm) REVERT: E 422 ASN cc_start: 0.8531 (m-40) cc_final: 0.8188 (m110) REVERT: E 461 LEU cc_start: 0.8610 (mt) cc_final: 0.8378 (mt) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.0745 time to fit residues: 20.2772 Evaluate side-chains 128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 101 GLN A 239 HIS A 305 GLN A 373 HIS A 380 GLN A 524 GLN A 598 GLN E 501 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.175347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.149235 restraints weight = 7898.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.148458 restraints weight = 9925.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.149655 restraints weight = 8752.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.150035 restraints weight = 6450.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.150276 restraints weight = 6467.400| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6682 Z= 0.175 Angle : 0.652 9.739 9093 Z= 0.340 Chirality : 0.047 0.299 961 Planarity : 0.005 0.035 1171 Dihedral : 5.914 53.943 967 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.73 % Allowed : 9.64 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.27), residues: 788 helix: -1.04 (0.23), residues: 400 sheet: -0.10 (0.60), residues: 59 loop : -0.10 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 169 TYR 0.024 0.002 TYR E 495 PHE 0.024 0.003 PHE E 497 TRP 0.024 0.002 TRP A 302 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6668) covalent geometry : angle 0.64848 ( 9064) SS BOND : bond 0.00370 ( 7) SS BOND : angle 1.21250 ( 14) hydrogen bonds : bond 0.04681 ( 283) hydrogen bonds : angle 5.29270 ( 797) metal coordination : bond 0.00090 ( 2) link_NAG-ASN : bond 0.00201 ( 5) link_NAG-ASN : angle 1.38321 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7282 (m-30) cc_final: 0.6975 (t0) REVERT: A 207 TYR cc_start: 0.8391 (m-80) cc_final: 0.7585 (m-10) REVERT: A 217 TYR cc_start: 0.8048 (t80) cc_final: 0.6592 (t80) REVERT: A 219 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7541 (mtm-85) REVERT: A 371 THR cc_start: 0.8499 (m) cc_final: 0.8236 (t) REVERT: A 483 GLU cc_start: 0.6313 (pt0) cc_final: 0.6061 (pt0) outliers start: 12 outliers final: 8 residues processed: 152 average time/residue: 0.0640 time to fit residues: 13.8960 Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 7.9990 chunk 40 optimal weight: 0.0070 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 380 GLN A 417 HIS A 508 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.170000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.142920 restraints weight = 12233.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.145274 restraints weight = 17192.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.147583 restraints weight = 10237.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.148927 restraints weight = 6483.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.149381 restraints weight = 5907.509| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6682 Z= 0.162 Angle : 0.600 7.570 9093 Z= 0.312 Chirality : 0.045 0.139 961 Planarity : 0.004 0.042 1171 Dihedral : 5.174 36.240 967 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.16 % Allowed : 12.37 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.31 (0.28), residues: 788 helix: -0.25 (0.25), residues: 395 sheet: -0.06 (0.65), residues: 51 loop : 0.07 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 161 TYR 0.019 0.002 TYR E 495 PHE 0.019 0.002 PHE E 515 TRP 0.019 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6668) covalent geometry : angle 0.59606 ( 9064) SS BOND : bond 0.00341 ( 7) SS BOND : angle 0.98826 ( 14) hydrogen bonds : bond 0.04336 ( 283) hydrogen bonds : angle 4.93400 ( 797) metal coordination : bond 0.00033 ( 2) link_NAG-ASN : bond 0.00122 ( 5) link_NAG-ASN : angle 1.59058 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7813 (tp30) cc_final: 0.7560 (tp30) REVERT: A 57 GLU cc_start: 0.7802 (tp30) cc_final: 0.7517 (tm-30) REVERT: A 67 ASP cc_start: 0.7299 (m-30) cc_final: 0.7004 (t0) REVERT: A 207 TYR cc_start: 0.8358 (m-80) cc_final: 0.7575 (m-10) REVERT: A 217 TYR cc_start: 0.8050 (t80) cc_final: 0.7625 (t80) REVERT: A 219 ARG cc_start: 0.8268 (mtm-85) cc_final: 0.7830 (mtm-85) REVERT: A 349 TRP cc_start: 0.8291 (m100) cc_final: 0.7924 (m100) REVERT: A 366 MET cc_start: 0.8385 (tmm) cc_final: 0.7931 (tmm) REVERT: A 371 THR cc_start: 0.8525 (m) cc_final: 0.8228 (t) REVERT: A 394 ASN cc_start: 0.7313 (t0) cc_final: 0.6254 (m110) REVERT: A 508 ASN cc_start: 0.8271 (m110) cc_final: 0.8052 (m110) REVERT: A 597 ASP cc_start: 0.7663 (t0) cc_final: 0.7248 (t0) REVERT: A 600 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8281 (mttm) REVERT: E 346 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7257 (ptp-110) REVERT: E 427 ASP cc_start: 0.8226 (m-30) cc_final: 0.8019 (m-30) REVERT: E 506 GLN cc_start: 0.8913 (mt0) cc_final: 0.8707 (mt0) outliers start: 14 outliers final: 11 residues processed: 117 average time/residue: 0.0636 time to fit residues: 10.5403 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.171230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.143463 restraints weight = 10163.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.143478 restraints weight = 9832.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.145272 restraints weight = 7971.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.146578 restraints weight = 4645.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.146758 restraints weight = 4334.942| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6682 Z= 0.143 Angle : 0.568 8.341 9093 Z= 0.291 Chirality : 0.043 0.144 961 Planarity : 0.004 0.040 1171 Dihedral : 4.763 36.769 967 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.01 % Allowed : 12.95 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.08 (0.29), residues: 788 helix: 0.17 (0.26), residues: 395 sheet: -0.08 (0.69), residues: 49 loop : 0.15 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.013 0.001 TYR E 495 PHE 0.014 0.002 PHE A 504 TRP 0.016 0.002 TRP A 594 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6668) covalent geometry : angle 0.56450 ( 9064) SS BOND : bond 0.00258 ( 7) SS BOND : angle 0.79796 ( 14) hydrogen bonds : bond 0.03842 ( 283) hydrogen bonds : angle 4.73405 ( 797) metal coordination : bond 0.00058 ( 2) link_NAG-ASN : bond 0.00131 ( 5) link_NAG-ASN : angle 1.47206 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8116 (tp30) cc_final: 0.7795 (tp30) REVERT: A 57 GLU cc_start: 0.7968 (tp30) cc_final: 0.7717 (tm-30) REVERT: A 67 ASP cc_start: 0.7410 (m-30) cc_final: 0.7070 (t0) REVERT: A 207 TYR cc_start: 0.8301 (m-80) cc_final: 0.7568 (m-10) REVERT: A 217 TYR cc_start: 0.8062 (t80) cc_final: 0.7821 (t80) REVERT: A 219 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7662 (mtm-85) REVERT: A 259 ILE cc_start: 0.8507 (pt) cc_final: 0.8136 (mt) REVERT: A 515 TYR cc_start: 0.7935 (m-10) cc_final: 0.7620 (m-10) REVERT: E 427 ASP cc_start: 0.8331 (m-30) cc_final: 0.8102 (m-30) REVERT: E 506 GLN cc_start: 0.8946 (mt0) cc_final: 0.8658 (mt0) outliers start: 13 outliers final: 11 residues processed: 112 average time/residue: 0.0641 time to fit residues: 10.2877 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 77 optimal weight: 0.0050 chunk 31 optimal weight: 0.0030 chunk 20 optimal weight: 0.0870 chunk 28 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** 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 = 0.3825 r_free = 0.3825 target = 0.175432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.153164 restraints weight = 14157.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.151976 restraints weight = 9630.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.148440 restraints weight = 7371.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.147670 restraints weight = 7659.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.147605 restraints weight = 7289.665| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6682 Z= 0.101 Angle : 0.518 8.076 9093 Z= 0.262 Chirality : 0.041 0.143 961 Planarity : 0.004 0.038 1171 Dihedral : 4.385 33.238 967 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.73 % Allowed : 13.81 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.46 (0.29), residues: 788 helix: 0.55 (0.26), residues: 395 sheet: 0.37 (0.85), residues: 37 loop : 0.20 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.015 0.001 TYR E 380 PHE 0.014 0.001 PHE A 356 TRP 0.013 0.001 TRP A 478 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6668) covalent geometry : angle 0.51602 ( 9064) SS BOND : bond 0.00228 ( 7) SS BOND : angle 0.74612 ( 14) hydrogen bonds : bond 0.03359 ( 283) hydrogen bonds : angle 4.48733 ( 797) metal coordination : bond 0.00044 ( 2) link_NAG-ASN : bond 0.00200 ( 5) link_NAG-ASN : angle 1.19104 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7840 (tp30) cc_final: 0.7519 (tp30) REVERT: A 207 TYR cc_start: 0.8089 (m-80) cc_final: 0.7365 (m-10) REVERT: A 219 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7528 (mtm-85) REVERT: A 222 LEU cc_start: 0.7842 (tp) cc_final: 0.7601 (tp) REVERT: A 259 ILE cc_start: 0.8367 (pt) cc_final: 0.8092 (mt) REVERT: A 366 MET cc_start: 0.8652 (tmm) cc_final: 0.8383 (tmm) REVERT: A 410 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7546 (mp) REVERT: E 444 LYS cc_start: 0.8979 (mttm) cc_final: 0.8468 (pttt) outliers start: 11 outliers final: 8 residues processed: 114 average time/residue: 0.0603 time to fit residues: 9.8316 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 484 GLN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.172796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.146084 restraints weight = 7933.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.144981 restraints weight = 9705.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.144668 restraints weight = 8906.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.144784 restraints weight = 7748.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.145278 restraints weight = 5989.022| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6682 Z= 0.133 Angle : 0.550 8.457 9093 Z= 0.281 Chirality : 0.043 0.143 961 Planarity : 0.004 0.038 1171 Dihedral : 4.387 30.904 967 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.30 % Allowed : 14.82 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.49 (0.29), residues: 788 helix: 0.66 (0.26), residues: 400 sheet: 0.03 (0.82), residues: 39 loop : 0.13 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.010 0.001 TYR E 396 PHE 0.014 0.001 PHE A 356 TRP 0.018 0.002 TRP A 478 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6668) covalent geometry : angle 0.54764 ( 9064) SS BOND : bond 0.00228 ( 7) SS BOND : angle 0.71339 ( 14) hydrogen bonds : bond 0.03507 ( 283) hydrogen bonds : angle 4.57098 ( 797) metal coordination : bond 0.00030 ( 2) link_NAG-ASN : bond 0.00171 ( 5) link_NAG-ASN : angle 1.28086 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7882 (tp30) cc_final: 0.7554 (tp30) REVERT: A 259 ILE cc_start: 0.8313 (pt) cc_final: 0.8046 (mt) REVERT: A 349 TRP cc_start: 0.8289 (m100) cc_final: 0.8013 (m100) REVERT: A 366 MET cc_start: 0.8657 (tmm) cc_final: 0.8392 (tmm) REVERT: E 489 TYR cc_start: 0.7574 (m-80) cc_final: 0.7271 (m-80) outliers start: 15 outliers final: 9 residues processed: 111 average time/residue: 0.0611 time to fit residues: 9.7111 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 484 GLN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 72 optimal weight: 0.0070 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.173129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.149534 restraints weight = 14293.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.151058 restraints weight = 19133.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.151037 restraints weight = 6588.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.151553 restraints weight = 5480.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.153094 restraints weight = 3539.596| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6682 Z= 0.103 Angle : 0.537 10.693 9093 Z= 0.267 Chirality : 0.041 0.145 961 Planarity : 0.004 0.037 1171 Dihedral : 4.180 30.719 967 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.44 % Allowed : 16.12 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.70 (0.30), residues: 788 helix: 0.85 (0.26), residues: 401 sheet: 0.42 (0.87), residues: 37 loop : 0.17 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.010 0.001 TYR E 508 PHE 0.017 0.001 PHE A 356 TRP 0.014 0.001 TRP A 478 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6668) covalent geometry : angle 0.53544 ( 9064) SS BOND : bond 0.00153 ( 7) SS BOND : angle 0.63996 ( 14) hydrogen bonds : bond 0.03205 ( 283) hydrogen bonds : angle 4.40908 ( 797) metal coordination : bond 0.00008 ( 2) link_NAG-ASN : bond 0.00218 ( 5) link_NAG-ASN : angle 1.12577 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7959 (tp30) cc_final: 0.7610 (tp30) REVERT: A 207 TYR cc_start: 0.8001 (m-80) cc_final: 0.7539 (m-10) REVERT: A 259 ILE cc_start: 0.8305 (pt) cc_final: 0.8076 (mt) REVERT: A 349 TRP cc_start: 0.8228 (m100) cc_final: 0.8010 (m100) REVERT: A 353 LYS cc_start: 0.8871 (mttt) cc_final: 0.8455 (mtpt) REVERT: A 366 MET cc_start: 0.8663 (tmm) cc_final: 0.8417 (tmm) REVERT: A 385 TYR cc_start: 0.8672 (p90) cc_final: 0.8429 (p90) outliers start: 9 outliers final: 8 residues processed: 107 average time/residue: 0.0636 time to fit residues: 9.5624 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 484 GLN Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 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 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.168981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.152186 restraints weight = 10271.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.147662 restraints weight = 16063.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.145433 restraints weight = 12172.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.145397 restraints weight = 12233.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.146063 restraints weight = 8113.127| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6682 Z= 0.167 Angle : 0.600 9.982 9093 Z= 0.304 Chirality : 0.044 0.167 961 Planarity : 0.004 0.037 1171 Dihedral : 4.444 31.893 967 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.73 % Allowed : 16.12 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.58 (0.30), residues: 788 helix: 0.77 (0.26), residues: 400 sheet: 0.15 (0.86), residues: 39 loop : 0.12 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 161 TYR 0.012 0.001 TYR E 453 PHE 0.017 0.002 PHE A 356 TRP 0.018 0.002 TRP A 473 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6668) covalent geometry : angle 0.59783 ( 9064) SS BOND : bond 0.00288 ( 7) SS BOND : angle 0.73279 ( 14) hydrogen bonds : bond 0.03655 ( 283) hydrogen bonds : angle 4.62224 ( 797) metal coordination : bond 0.00035 ( 2) link_NAG-ASN : bond 0.00138 ( 5) link_NAG-ASN : angle 1.40347 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7975 (tp30) cc_final: 0.7617 (tp30) REVERT: A 259 ILE cc_start: 0.8372 (pt) cc_final: 0.8102 (mt) REVERT: A 366 MET cc_start: 0.8666 (tmm) cc_final: 0.8364 (tmm) REVERT: A 385 TYR cc_start: 0.8777 (p90) cc_final: 0.8478 (p90) REVERT: A 564 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8535 (mm-30) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.0635 time to fit residues: 9.3661 Evaluate side-chains 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 484 GLN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 30 optimal weight: 0.0020 chunk 45 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 0.0050 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.171175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.151201 restraints weight = 14646.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.152029 restraints weight = 20777.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.151401 restraints weight = 7481.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.152163 restraints weight = 6145.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.152600 restraints weight = 4300.334| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6682 Z= 0.119 Angle : 0.563 10.195 9093 Z= 0.281 Chirality : 0.042 0.152 961 Planarity : 0.004 0.036 1171 Dihedral : 4.286 33.287 967 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.44 % Allowed : 17.12 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.73 (0.30), residues: 788 helix: 0.93 (0.26), residues: 400 sheet: 0.43 (0.92), residues: 37 loop : 0.11 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.011 0.001 TYR E 508 PHE 0.017 0.001 PHE A 356 TRP 0.017 0.001 TRP A 478 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6668) covalent geometry : angle 0.56050 ( 9064) SS BOND : bond 0.00188 ( 7) SS BOND : angle 0.62515 ( 14) hydrogen bonds : bond 0.03337 ( 283) hydrogen bonds : angle 4.51636 ( 797) metal coordination : bond 0.00047 ( 2) link_NAG-ASN : bond 0.00175 ( 5) link_NAG-ASN : angle 1.29759 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.167 Fit side-chains REVERT: A 35 GLU cc_start: 0.7952 (tp30) cc_final: 0.7651 (tp30) REVERT: A 207 TYR cc_start: 0.8136 (m-80) cc_final: 0.7498 (m-10) REVERT: A 353 LYS cc_start: 0.8874 (mttt) cc_final: 0.8504 (mtpt) REVERT: A 385 TYR cc_start: 0.8630 (p90) cc_final: 0.8393 (p90) REVERT: A 508 ASN cc_start: 0.8273 (m110) cc_final: 0.8050 (m110) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.0642 time to fit residues: 9.5484 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 484 GLN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 74 optimal weight: 0.0670 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.171707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.147272 restraints weight = 14583.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.150332 restraints weight = 22287.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.151410 restraints weight = 9421.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.152213 restraints weight = 6100.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.152748 restraints weight = 4437.643| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6682 Z= 0.121 Angle : 0.567 10.763 9093 Z= 0.281 Chirality : 0.042 0.164 961 Planarity : 0.004 0.035 1171 Dihedral : 4.246 32.971 967 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.44 % Allowed : 17.55 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.30), residues: 788 helix: 1.00 (0.26), residues: 400 sheet: 0.43 (0.91), residues: 37 loop : 0.11 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.009 0.001 TYR E 508 PHE 0.010 0.001 PHE E 429 TRP 0.014 0.001 TRP A 302 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6668) covalent geometry : angle 0.56439 ( 9064) SS BOND : bond 0.00173 ( 7) SS BOND : angle 0.63907 ( 14) hydrogen bonds : bond 0.03327 ( 283) hydrogen bonds : angle 4.47181 ( 797) metal coordination : bond 0.00049 ( 2) link_NAG-ASN : bond 0.00179 ( 5) link_NAG-ASN : angle 1.30417 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.266 Fit side-chains REVERT: A 35 GLU cc_start: 0.7936 (tp30) cc_final: 0.7680 (tp30) REVERT: A 207 TYR cc_start: 0.8147 (m-80) cc_final: 0.7530 (m-10) REVERT: A 323 MET cc_start: 0.7921 (mmm) cc_final: 0.7654 (mmm) REVERT: A 353 LYS cc_start: 0.8892 (mttt) cc_final: 0.8498 (mtpt) REVERT: A 385 TYR cc_start: 0.8600 (p90) cc_final: 0.8354 (p90) outliers start: 9 outliers final: 9 residues processed: 105 average time/residue: 0.0631 time to fit residues: 9.4907 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 484 GLN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.0060 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.170789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.156411 restraints weight = 11783.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.150160 restraints weight = 18350.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.147504 restraints weight = 11417.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.149125 restraints weight = 9266.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.149671 restraints weight = 5863.949| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6682 Z= 0.131 Angle : 0.573 10.584 9093 Z= 0.286 Chirality : 0.042 0.151 961 Planarity : 0.004 0.036 1171 Dihedral : 4.260 32.953 967 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.44 % Allowed : 17.27 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.74 (0.30), residues: 788 helix: 0.98 (0.26), residues: 400 sheet: 0.40 (0.92), residues: 37 loop : 0.07 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.016 0.001 TYR A 515 PHE 0.018 0.002 PHE A 356 TRP 0.015 0.001 TRP A 478 HIS 0.005 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6668) covalent geometry : angle 0.57101 ( 9064) SS BOND : bond 0.00198 ( 7) SS BOND : angle 0.66395 ( 14) hydrogen bonds : bond 0.03382 ( 283) hydrogen bonds : angle 4.48708 ( 797) metal coordination : bond 0.00042 ( 2) link_NAG-ASN : bond 0.00155 ( 5) link_NAG-ASN : angle 1.28399 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1278.92 seconds wall clock time: 22 minutes 39.36 seconds (1359.36 seconds total)