Starting phenix.real_space_refine on Fri Sep 11 01:36:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vx5_32169/09_2026/7vx5_32169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx5_32169/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7vx5_32169/09_2026/7vx5_32169.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vx5_32169/09_2026/7vx5_32169.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vx5_32169/09_2026/7vx5_32169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx5_32169/09_2026/7vx5_32169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vx5_32169/09_2026/7vx5_32169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx5_32169/09_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-2.2.1-6174/lib/python3.11/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 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 chiralities: 1 Time building chain proxies: 2.29, per 1000 atoms: 0.35 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: 0.50 Conformation dependent library (CDL) restraints added in 492.1 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: 0.19 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: 0.93 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 3778 15.98 - 31.96: 85 31.96 - 47.95: 23 47.95 - 63.93: 6 63.93 - 79.91: 3 Dihedral angle restraints: 3895 sinusoidal: 1571 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 3892 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: 3.380 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.940 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 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 : 8.618 79.909 2384 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/Z covalent geometry : bond 0.00321 / 0.18 ( 6668) covalent geometry : angle 0.65192 / 0.42 ( 9064) SS BOND : bond 0.00229 / 0.12 ( 7) SS BOND : angle 0.95133 / 0.56 ( 14) hydrogen bonds : bond 0.29514 / 18.96 ( 283) hydrogen bonds : angle 9.43504 / 6.56 ( 797) metal coordination : bond 0.06436 / 3.38 ( 2) link_NAG-ASN : bond 0.00148 / 0.09 ( 5) link_NAG-ASN : angle 1.44606 / 0.88 ( 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 : 0.237 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: 0.0753 time to fit residues: 20.7025 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 : 0.289 ------------------------------------------------------------------------------- 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... 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 = 0.175378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.149376 restraints weight = 7908.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.148992 restraints weight = 10566.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.150069 restraints weight = 8719.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.150157 restraints weight = 6458.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.150567 restraints weight = 6233.174| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6682 Z= 0.175 Angle : 0.649 9.632 9093 Z= 0.340 Chirality : 0.047 0.329 961 Planarity : 0.005 0.035 1171 Dihedral : 4.674 17.345 862 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.87 % Allowed : 9.35 % Favored : 88.78 % 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: -1.03 (0.23), residues: 400 sheet: -0.10 (0.60), residues: 59 loop : -0.11 (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 0.025 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/Z covalent geometry : bond 0.00398 / 0.17 ( 6668) covalent geometry : angle 0.64672 / 0.34 ( 9064) SS BOND : bond 0.00928 / 0.47 ( 7) SS BOND : angle 1.13011 / 0.60 ( 14) hydrogen bonds : bond 0.04654 / 3.01 ( 283) hydrogen bonds : angle 5.28701 / 3.71 ( 797) metal coordination : bond 0.00057 / 0.03 ( 2) link_NAG-ASN : bond 0.00227 / 0.12 ( 5) link_NAG-ASN : angle 1.32507 / 0.79 ( 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: 13 poor density : 145 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7320 (m-30) cc_final: 0.6985 (t0) REVERT: A 194 ASN cc_start: 0.7129 (OUTLIER) cc_final: 0.6907 (t0) REVERT: A 207 TYR cc_start: 0.8376 (m-80) cc_final: 0.7560 (m-10) REVERT: A 217 TYR cc_start: 0.8072 (t80) cc_final: 0.6594 (t80) REVERT: A 219 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: A 371 THR cc_start: 0.8495 (m) cc_final: 0.8222 (t) REVERT: A 483 GLU cc_start: 0.6320 (pt0) cc_final: 0.6072 (pt0) outliers start: 13 outliers final: 8 residues processed: 151 average time/residue: 0.0643 time to fit residues: 13.8856 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 194 ASN 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: 8.9990 chunk 40 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 65 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 380 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.174683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.151842 restraints weight = 11862.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.151367 restraints weight = 17716.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.152159 restraints weight = 7728.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.152842 restraints weight = 6384.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.153943 restraints weight = 4614.888| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6682 Z= 0.143 Angle : 0.580 7.838 9093 Z= 0.301 Chirality : 0.043 0.143 961 Planarity : 0.004 0.041 1171 Dihedral : 4.380 16.229 862 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.87 % Allowed : 12.66 % 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: -0.24 (0.28), residues: 788 helix: -0.22 (0.25), residues: 395 sheet: 0.07 (0.66), residues: 51 loop : 0.12 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 161 TYR 0.018 0.001 TYR E 495 PHE 0.017 0.002 PHE E 497 TRP 0.022 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6668) covalent geometry : angle 0.57722 / 0.30 ( 9064) SS BOND : bond 0.00283 / 0.15 ( 7) SS BOND : angle 0.95721 / 0.51 ( 14) hydrogen bonds : bond 0.04226 / 2.74 ( 283) hydrogen bonds : angle 4.87970 / 3.42 ( 797) metal coordination : bond 0.00020 / 0.01 ( 2) link_NAG-ASN : bond 0.00120 / 0.06 ( 5) link_NAG-ASN : angle 1.31864 / 0.78 ( 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 123 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7754 (tp30) cc_final: 0.7509 (tm-30) REVERT: A 67 ASP cc_start: 0.7258 (m-30) cc_final: 0.7044 (t0) REVERT: A 207 TYR cc_start: 0.8279 (m-80) cc_final: 0.7573 (m-10) REVERT: A 217 TYR cc_start: 0.8021 (t80) cc_final: 0.7686 (t80) REVERT: A 219 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7812 (mtm-85) REVERT: A 366 MET cc_start: 0.8361 (tmm) cc_final: 0.7895 (tmm) REVERT: A 394 ASN cc_start: 0.7227 (t0) cc_final: 0.6217 (m110) REVERT: A 515 TYR cc_start: 0.7667 (m-80) cc_final: 0.7441 (m-10) REVERT: E 506 GLN cc_start: 0.8796 (mt0) cc_final: 0.8569 (mt0) outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.0610 time to fit residues: 10.5137 Evaluate side-chains 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 168 TRP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 443 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: 1.9990 chunk 61 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN E 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.173277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.144688 restraints weight = 10134.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.146795 restraints weight = 12732.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.148607 restraints weight = 9252.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.149201 restraints weight = 6008.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.150446 restraints weight = 5373.206| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6682 Z= 0.134 Angle : 0.558 8.743 9093 Z= 0.286 Chirality : 0.043 0.142 961 Planarity : 0.004 0.043 1171 Dihedral : 4.208 15.972 862 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 13.81 % Favored : 84.03 % 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: 0.09 (0.29), residues: 788 helix: 0.18 (0.25), residues: 402 sheet: -0.00 (0.69), residues: 49 loop : 0.16 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.014 0.001 TYR E 495 PHE 0.014 0.002 PHE A 504 TRP 0.024 0.002 TRP A 594 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 6668) covalent geometry : angle 0.55602 / 0.29 ( 9064) SS BOND : bond 0.00255 / 0.13 ( 7) SS BOND : angle 0.77970 / 0.41 ( 14) hydrogen bonds : bond 0.03801 / 2.49 ( 283) hydrogen bonds : angle 4.69798 / 3.30 ( 797) metal coordination : bond 0.00060 / 0.03 ( 2) link_NAG-ASN : bond 0.00146 / 0.08 ( 5) link_NAG-ASN : angle 1.20024 / 0.72 ( 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 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8276 (tp30) cc_final: 0.8051 (tp30) REVERT: A 57 GLU cc_start: 0.7821 (tp30) cc_final: 0.7612 (tm-30) REVERT: A 67 ASP cc_start: 0.7373 (m-30) cc_final: 0.7113 (t0) REVERT: A 207 TYR cc_start: 0.8232 (m-80) cc_final: 0.7491 (m-10) REVERT: A 217 TYR cc_start: 0.8045 (t80) cc_final: 0.7824 (t80) REVERT: A 219 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7677 (mtm-85) REVERT: A 259 ILE cc_start: 0.8459 (pt) cc_final: 0.8074 (mt) REVERT: A 394 ASN cc_start: 0.7346 (t0) cc_final: 0.6123 (m110) REVERT: E 506 GLN cc_start: 0.8938 (mt0) cc_final: 0.8619 (mt0) outliers start: 14 outliers final: 13 residues processed: 109 average time/residue: 0.0620 time to fit residues: 9.6746 Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 168 TRP 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 387 LEU 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: 0.9990 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 77 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.0535 > 50:) chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3769 r_free = 0.3769 target = 0.168761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.138928 restraints weight = 14611.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.143888 restraints weight = 19370.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.146124 restraints weight = 7107.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.147952 restraints weight = 5443.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.148806 restraints weight = 3969.733| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6682 Z= 0.164 Angle : 0.575 8.287 9093 Z= 0.296 Chirality : 0.044 0.143 961 Planarity : 0.004 0.041 1171 Dihedral : 4.353 18.000 862 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.45 % Allowed : 14.10 % Favored : 83.45 % 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: 0.22 (0.29), residues: 788 helix: 0.39 (0.26), residues: 396 sheet: -0.09 (0.82), residues: 39 loop : 0.09 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 161 TYR 0.013 0.002 TYR E 453 PHE 0.015 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/Z covalent geometry : bond 0.00384 / 0.16 ( 6668) covalent geometry : angle 0.57238 / 0.30 ( 9064) SS BOND : bond 0.00313 / 0.16 ( 7) SS BOND : angle 0.77985 / 0.41 ( 14) hydrogen bonds : bond 0.03876 / 2.52 ( 283) hydrogen bonds : angle 4.77352 / 3.37 ( 797) metal coordination : bond 0.00061 / 0.03 ( 2) link_NAG-ASN : bond 0.00147 / 0.08 ( 5) link_NAG-ASN : angle 1.31510 / 0.80 ( 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 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8289 (tp30) cc_final: 0.7891 (tm-30) REVERT: A 174 LYS cc_start: 0.7455 (mmtp) cc_final: 0.7246 (mmtm) REVERT: A 219 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7656 (mtm-85) REVERT: A 259 ILE cc_start: 0.8405 (pt) cc_final: 0.8084 (mt) REVERT: A 366 MET cc_start: 0.8680 (tmm) cc_final: 0.8396 (tmm) REVERT: A 394 ASN cc_start: 0.7426 (t0) cc_final: 0.6267 (m110) outliers start: 16 outliers final: 14 residues processed: 105 average time/residue: 0.0632 time to fit residues: 9.6334 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 168 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain E residue 359 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 0.0070 chunk 47 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3774 r_free = 0.3774 target = 0.167730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.154128 restraints weight = 8021.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.150617 restraints weight = 10103.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.148843 restraints weight = 11340.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.148625 restraints weight = 12633.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.148490 restraints weight = 11028.813| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6682 Z= 0.158 Angle : 0.576 7.837 9093 Z= 0.298 Chirality : 0.044 0.142 961 Planarity : 0.004 0.040 1171 Dihedral : 4.313 17.583 862 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.73 % Allowed : 15.68 % Favored : 81.58 % 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: 0.23 (0.29), residues: 788 helix: 0.43 (0.26), residues: 399 sheet: -0.24 (0.84), residues: 39 loop : 0.07 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.012 0.001 TYR E 453 PHE 0.014 0.002 PHE E 429 TRP 0.019 0.002 TRP A 478 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 6668) covalent geometry : angle 0.57351 / 0.30 ( 9064) SS BOND : bond 0.00270 / 0.14 ( 7) SS BOND : angle 0.70732 / 0.38 ( 14) hydrogen bonds : bond 0.03746 / 2.44 ( 283) hydrogen bonds : angle 4.78569 / 3.38 ( 797) metal coordination : bond 0.00077 / 0.04 ( 2) link_NAG-ASN : bond 0.00137 / 0.07 ( 5) link_NAG-ASN : angle 1.30263 / 0.80 ( 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7607 (mtm-85) REVERT: A 259 ILE cc_start: 0.8146 (pt) cc_final: 0.7908 (mt) REVERT: A 349 TRP cc_start: 0.8270 (m100) cc_final: 0.7984 (m100) REVERT: A 366 MET cc_start: 0.8566 (tmm) cc_final: 0.8345 (tmm) outliers start: 18 outliers final: 16 residues processed: 106 average time/residue: 0.0657 time to fit residues: 10.1010 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 168 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 365 THR 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 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: 0.6980 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3769 r_free = 0.3769 target = 0.167391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.153430 restraints weight = 14576.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.148439 restraints weight = 14722.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.146257 restraints weight = 16574.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.148006 restraints weight = 12674.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.148127 restraints weight = 8325.791| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6682 Z= 0.152 Angle : 0.578 8.103 9093 Z= 0.298 Chirality : 0.044 0.142 961 Planarity : 0.004 0.038 1171 Dihedral : 4.276 16.297 862 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.02 % Allowed : 15.25 % Favored : 81.73 % 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 (0.30), residues: 788 helix: 0.52 (0.26), residues: 399 sheet: -0.05 (0.85), residues: 39 loop : 0.04 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.011 0.001 TYR E 453 PHE 0.013 0.002 PHE E 429 TRP 0.019 0.002 TRP A 478 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 6668) covalent geometry : angle 0.57587 / 0.30 ( 9064) SS BOND : bond 0.00251 / 0.13 ( 7) SS BOND : angle 0.69262 / 0.37 ( 14) hydrogen bonds : bond 0.03716 / 2.42 ( 283) hydrogen bonds : angle 4.75150 / 3.36 ( 797) metal coordination : bond 0.00123 / 0.06 ( 2) link_NAG-ASN : bond 0.00138 / 0.07 ( 5) link_NAG-ASN : angle 1.21542 / 0.74 ( 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 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8390 (m-10) cc_final: 0.7761 (m-10) REVERT: A 219 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: A 259 ILE cc_start: 0.8297 (pt) cc_final: 0.8036 (mt) REVERT: A 270 MET cc_start: 0.4978 (tpt) cc_final: 0.4711 (tpp) REVERT: A 349 TRP cc_start: 0.8217 (m100) cc_final: 0.7987 (m100) REVERT: A 366 MET cc_start: 0.8639 (tmm) cc_final: 0.8377 (tmm) outliers start: 20 outliers final: 16 residues processed: 101 average time/residue: 0.0691 time to fit residues: 10.0048 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 168 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 359 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.167497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.141104 restraints weight = 10246.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.144606 restraints weight = 16404.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.146376 restraints weight = 8184.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.146764 restraints weight = 6002.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.147472 restraints weight = 5308.778| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6682 Z= 0.178 Angle : 0.613 10.194 9093 Z= 0.312 Chirality : 0.045 0.164 961 Planarity : 0.004 0.038 1171 Dihedral : 4.429 17.123 862 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.73 % Allowed : 15.25 % Favored : 82.01 % 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: 0.24 (0.30), residues: 788 helix: 0.56 (0.26), residues: 393 sheet: -0.28 (0.85), residues: 40 loop : -0.08 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 460 TYR 0.014 0.002 TYR A 515 PHE 0.018 0.002 PHE A 356 TRP 0.021 0.002 TRP A 478 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 6668) covalent geometry : angle 0.61066 / 0.31 ( 9064) SS BOND : bond 0.00314 / 0.17 ( 7) SS BOND : angle 0.75302 / 0.40 ( 14) hydrogen bonds : bond 0.03925 / 2.54 ( 283) hydrogen bonds : angle 4.83609 / 3.44 ( 797) metal coordination : bond 0.00048 / 0.02 ( 2) link_NAG-ASN : bond 0.00124 / 0.06 ( 5) link_NAG-ASN : angle 1.35439 / 0.82 ( 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 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7915 (mtm-85) REVERT: A 366 MET cc_start: 0.8702 (tmm) cc_final: 0.8459 (tmm) REVERT: A 480 MET cc_start: 0.6887 (ttm) cc_final: 0.6533 (ttm) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.0700 time to fit residues: 10.0489 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 168 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 359 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 71 optimal weight: 0.0040 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3791 r_free = 0.3791 target = 0.170866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.140592 restraints weight = 14532.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.145830 restraints weight = 19100.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.147767 restraints weight = 7044.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.150242 restraints weight = 5107.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.150468 restraints weight = 3920.436| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5814 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= 0.128 Angle : 0.579 9.243 9093 Z= 0.291 Chirality : 0.042 0.151 961 Planarity : 0.004 0.037 1171 Dihedral : 4.194 15.982 862 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.01 % Allowed : 16.12 % Favored : 81.87 % 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: 0.38 (0.30), residues: 788 helix: 0.64 (0.26), residues: 401 sheet: 0.13 (0.90), residues: 37 loop : -0.03 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.013 0.001 TYR A 515 PHE 0.021 0.001 PHE A 356 TRP 0.015 0.002 TRP A 478 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6668) covalent geometry : angle 0.57718 / 0.29 ( 9064) SS BOND : bond 0.00192 / 0.10 ( 7) SS BOND : angle 0.66315 / 0.35 ( 14) hydrogen bonds : bond 0.03557 / 2.31 ( 283) hydrogen bonds : angle 4.66744 / 3.31 ( 797) metal coordination : bond 0.00036 / 0.02 ( 2) link_NAG-ASN : bond 0.00201 / 0.11 ( 5) link_NAG-ASN : angle 1.12718 / 0.69 ( 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 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.252 Fit side-chains REVERT: A 207 TYR cc_start: 0.8154 (m-10) cc_final: 0.7495 (m-10) REVERT: A 353 LYS cc_start: 0.8830 (mttt) cc_final: 0.8441 (mtpt) REVERT: A 385 TYR cc_start: 0.8771 (p90) cc_final: 0.8478 (p90) REVERT: A 480 MET cc_start: 0.6783 (ttm) cc_final: 0.6450 (ttm) REVERT: A 504 PHE cc_start: 0.7875 (t80) cc_final: 0.7661 (t80) REVERT: A 508 ASN cc_start: 0.8331 (m110) cc_final: 0.8105 (m110) REVERT: A 564 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8587 (mm-30) outliers start: 13 outliers final: 12 residues processed: 101 average time/residue: 0.0629 time to fit residues: 9.1652 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 259 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 359 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 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 66 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3806 r_free = 0.3806 target = 0.172288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.141667 restraints weight = 14459.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.147506 restraints weight = 18599.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.149338 restraints weight = 6474.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.151976 restraints weight = 4813.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.152103 restraints weight = 3716.809| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6682 Z= 0.119 Angle : 0.586 10.475 9093 Z= 0.293 Chirality : 0.041 0.148 961 Planarity : 0.004 0.036 1171 Dihedral : 4.065 15.481 862 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.01 % Allowed : 16.83 % Favored : 81.15 % 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: 0.53 (0.30), residues: 788 helix: 0.81 (0.26), residues: 399 sheet: 0.17 (0.90), residues: 37 loop : -0.02 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.014 0.001 TYR E 380 PHE 0.011 0.001 PHE A 356 TRP 0.015 0.002 TRP A 478 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6668) covalent geometry : angle 0.58515 / 0.29 ( 9064) SS BOND : bond 0.00233 / 0.12 ( 7) SS BOND : angle 0.70445 / 0.38 ( 14) hydrogen bonds : bond 0.03448 / 2.24 ( 283) hydrogen bonds : angle 4.60553 / 3.27 ( 797) metal coordination : bond 0.00042 / 0.02 ( 2) link_NAG-ASN : bond 0.00218 / 0.12 ( 5) link_NAG-ASN : angle 0.98919 / 0.61 ( 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 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.233 Fit side-chains REVERT: A 207 TYR cc_start: 0.8052 (m-10) cc_final: 0.7626 (m-10) REVERT: A 219 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7715 (ttm110) REVERT: A 353 LYS cc_start: 0.8832 (mttt) cc_final: 0.8423 (mtpt) REVERT: A 385 TYR cc_start: 0.8816 (p90) cc_final: 0.8474 (p90) REVERT: A 480 MET cc_start: 0.6778 (ttm) cc_final: 0.6518 (ttm) REVERT: A 504 PHE cc_start: 0.7827 (t80) cc_final: 0.7595 (t80) REVERT: A 564 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8577 (mm-30) outliers start: 13 outliers final: 12 residues processed: 99 average time/residue: 0.0730 time to fit residues: 10.1456 Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 168 TRP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 468 ILE 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 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.0370 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 0.0270 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 0.0070 chunk 40 optimal weight: 0.0470 overall best weight: 0.1632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN A 139 GLN A 508 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.173524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.146261 restraints weight = 11421.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.151366 restraints weight = 16896.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.153490 restraints weight = 6794.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.154642 restraints weight = 5377.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.155539 restraints weight = 4092.748| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6682 Z= 0.110 Angle : 0.586 10.832 9093 Z= 0.292 Chirality : 0.041 0.148 961 Planarity : 0.004 0.037 1171 Dihedral : 3.983 16.300 862 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.58 % Allowed : 17.84 % Favored : 80.58 % 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: 0.64 (0.30), residues: 788 helix: 0.93 (0.27), residues: 398 sheet: 0.28 (0.91), residues: 37 loop : -0.01 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 393 TYR 0.015 0.001 TYR E 380 PHE 0.016 0.001 PHE A 356 TRP 0.016 0.001 TRP A 478 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6668) covalent geometry : angle 0.58495 / 0.29 ( 9064) SS BOND : bond 0.00158 / 0.08 ( 7) SS BOND : angle 0.64166 / 0.35 ( 14) hydrogen bonds : bond 0.03289 / 2.14 ( 283) hydrogen bonds : angle 4.53611 / 3.22 ( 797) metal coordination : bond 0.00015 / 0.01 ( 2) link_NAG-ASN : bond 0.00216 / 0.12 ( 5) link_NAG-ASN : angle 0.93606 / 0.57 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1276.21 seconds wall clock time: 22 minutes 43.25 seconds (1363.25 seconds total)