Starting phenix.real_space_refine on Tue Feb 11 20:01:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vx5_32169/02_2025/7vx5_32169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx5_32169/02_2025/7vx5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vx5_32169/02_2025/7vx5_32169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx5_32169/02_2025/7vx5_32169.map" model { file = "/net/cci-nas-00/data/ceres_data/7vx5_32169/02_2025/7vx5_32169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx5_32169/02_2025/7vx5_32169.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6487 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.40, per 1000 atoms: 1.14 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: 1.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.66 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: 1.77 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2080 1.34 - 1.46: 1694 1.46 - 1.58: 2836 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6668 Sorted by residual: bond pdb=" C LYS E 424 " pdb=" N LEU E 425 " ideal model delta sigma weight residual 1.331 1.374 -0.043 2.07e-02 2.33e+03 4.35e+00 bond pdb=" CA CYS E 336 " pdb=" C CYS E 336 " ideal model delta sigma weight residual 1.526 1.505 0.021 1.14e-02 7.69e+03 3.41e+00 bond pdb=" CA GLN E 484 " pdb=" C GLN E 484 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.38e-02 5.25e+03 2.57e+00 bond pdb=" C ALA A 36 " pdb=" N GLU A 37 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.31e-02 5.83e+03 2.35e+00 bond pdb=" CA VAL E 445 " pdb=" C VAL E 445 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.35e-02 5.49e+03 2.27e+00 ... (remaining 6663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 8677 1.49 - 2.99: 347 2.99 - 4.48: 34 4.48 - 5.97: 5 5.97 - 7.46: 1 Bond angle restraints: 9064 Sorted by residual: angle pdb=" N GLY E 446 " pdb=" CA GLY E 446 " pdb=" C GLY E 446 " ideal model delta sigma weight residual 115.36 107.90 7.46 1.33e+00 5.65e-01 3.15e+01 angle pdb=" N GLY A 147 " pdb=" CA GLY A 147 " pdb=" C GLY A 147 " ideal model delta sigma weight residual 112.64 117.74 -5.10 1.21e+00 6.83e-01 1.78e+01 angle pdb=" C VAL E 445 " pdb=" CA VAL E 445 " pdb=" CB VAL E 445 " ideal model delta sigma weight residual 111.32 105.41 5.91 1.63e+00 3.76e-01 1.31e+01 angle pdb=" C TYR E 495 " pdb=" N GLY E 496 " pdb=" CA GLY E 496 " ideal model delta sigma weight residual 120.98 117.78 3.20 9.00e-01 1.23e+00 1.27e+01 angle pdb=" C ALA A 36 " pdb=" N GLU A 37 " pdb=" CA GLU A 37 " ideal model delta sigma weight residual 120.28 116.09 4.19 1.34e+00 5.57e-01 9.78e+00 ... (remaining 9059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 3869 15.98 - 31.96: 89 31.96 - 47.95: 29 47.95 - 63.93: 10 63.93 - 79.91: 3 Dihedral angle restraints: 4000 sinusoidal: 1676 harmonic: 2324 Sorted by residual: dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N GLY A 147 " pdb=" CA GLY A 147 " ideal model delta harmonic sigma weight residual 180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA E 352 " pdb=" C ALA E 352 " pdb=" N TRP E 353 " pdb=" CA TRP E 353 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TYR A 497 " pdb=" C TYR A 497 " pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 760 0.050 - 0.100: 167 0.100 - 0.150: 30 0.150 - 0.200: 3 0.200 - 0.250: 1 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA VAL E 445 " pdb=" N VAL E 445 " pdb=" C VAL E 445 " pdb=" CB VAL E 445 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA GLN E 498 " pdb=" N GLN E 498 " pdb=" C GLN E 498 " pdb=" CB GLN E 498 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA GLU A 37 " pdb=" N GLU A 37 " pdb=" C GLU A 37 " pdb=" CB GLU A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 958 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 498 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO E 499 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 499 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 499 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 583 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 484 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C GLN E 484 " -0.025 2.00e-02 2.50e+03 pdb=" O GLN E 484 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY E 485 " 0.008 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1458 2.78 - 3.31: 6109 3.31 - 3.84: 10401 3.84 - 4.37: 12459 4.37 - 4.90: 21156 Nonbonded interactions: 51583 Sorted by model distance: nonbonded pdb=" OH TYR A 83 " pdb=" OD1 ASN E 487 " model vdw 2.246 3.040 nonbonded pdb=" N SER A 19 " pdb=" OE1 GLU A 23 " model vdw 2.264 3.120 nonbonded pdb=" O MET A 152 " pdb=" NH1 ARG A 161 " model vdw 2.270 3.120 nonbonded pdb=" OD1 ASN A 394 " pdb=" N GLY A 395 " model vdw 2.275 3.120 nonbonded pdb=" O MET A 190 " pdb=" ND2 ASN A 194 " model vdw 2.279 3.120 ... (remaining 51578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.550 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6668 Z= 0.210 Angle : 0.652 7.463 9064 Z= 0.422 Chirality : 0.044 0.250 961 Planarity : 0.004 0.065 1171 Dihedral : 9.062 79.909 2489 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.001 TRP A 302 HIS 0.003 0.001 HIS A 535 PHE 0.020 0.002 PHE E 497 TYR 0.025 0.001 TYR E 495 ARG 0.004 0.000 ARG A 169 *********************** 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 : 1.038 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: 0.8069 (mt) cc_final: 0.7866 (mp) REVERT: A 98 GLN cc_start: 0.8329 (tt0) cc_final: 0.7716 (mm110) REVERT: A 217 TYR cc_start: 0.8174 (t80) cc_final: 0.7329 (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: 0.2263 (tpp) REVERT: A 323 MET cc_start: 0.7078 (mmp) cc_final: 0.5948 (mmt) REVERT: A 411 SER cc_start: 0.8513 (m) cc_final: 0.8296 (p) REVERT: A 513 ILE cc_start: 0.6925 (tp) cc_final: 0.6478 (tt) REVERT: A 531 GLN cc_start: 0.7367 (tt0) cc_final: 0.7057 (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: 0.1969 time to fit residues: 52.6675 Evaluate side-chains 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 32 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.0470 chunk 45 optimal weight: 0.3980 chunk 70 optimal weight: 0.0010 overall best weight: 0.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 101 GLN A 239 HIS A 305 GLN A 373 HIS A 380 GLN A 524 GLN E 501 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.181315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.160948 restraints weight = 15584.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.163239 restraints weight = 18106.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.164794 restraints weight = 6899.529| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6668 Z= 0.174 Angle : 0.600 9.610 9064 Z= 0.313 Chirality : 0.044 0.250 961 Planarity : 0.005 0.032 1171 Dihedral : 5.778 55.015 967 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 1.29 % Allowed : 10.07 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.28), residues: 788 helix: -0.91 (0.23), residues: 393 sheet: 0.50 (0.70), residues: 46 loop : -0.00 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 302 HIS 0.005 0.001 HIS A 34 PHE 0.022 0.002 PHE A 315 TYR 0.024 0.002 TYR E 495 ARG 0.007 0.001 ARG A 169 *********************** 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 146 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7182 (m-30) cc_final: 0.6966 (t0) REVERT: A 194 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6680 (t0) REVERT: A 207 TYR cc_start: 0.8237 (m-80) cc_final: 0.7529 (m-10) REVERT: A 217 TYR cc_start: 0.8090 (t80) cc_final: 0.7657 (t80) REVERT: A 219 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7357 (mtm-85) REVERT: A 270 MET cc_start: 0.3171 (tpp) cc_final: 0.2559 (tpp) REVERT: A 360 MET cc_start: 0.6485 (tmm) cc_final: 0.6052 (ttm) REVERT: A 366 MET cc_start: 0.8223 (tmm) cc_final: 0.7660 (tmm) REVERT: E 347 PHE cc_start: 0.8257 (m-10) cc_final: 0.8017 (m-80) outliers start: 9 outliers final: 8 residues processed: 144 average time/residue: 0.1706 time to fit residues: 33.7530 Evaluate side-chains 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 494 SER Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.0000 chunk 6 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 380 GLN A 417 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.172333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.144999 restraints weight = 11521.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.148706 restraints weight = 16062.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.150648 restraints weight = 8223.251| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 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 = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6668 Z= 0.235 Angle : 0.611 7.707 9064 Z= 0.316 Chirality : 0.046 0.203 961 Planarity : 0.004 0.038 1171 Dihedral : 5.204 42.731 967 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.59 % Allowed : 12.81 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.28), residues: 788 helix: -0.21 (0.25), residues: 396 sheet: -0.36 (0.59), residues: 58 loop : 0.13 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 594 HIS 0.004 0.001 HIS A 378 PHE 0.020 0.002 PHE E 515 TYR 0.021 0.002 TYR E 495 ARG 0.004 0.001 ARG A 161 *********************** 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 129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7352 (m-30) cc_final: 0.7042 (t0) REVERT: A 217 TYR cc_start: 0.8021 (t80) cc_final: 0.7721 (t80) REVERT: A 219 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7843 (mtm-85) REVERT: A 360 MET cc_start: 0.6546 (tmm) cc_final: 0.6034 (ttm) REVERT: A 366 MET cc_start: 0.8337 (tmm) cc_final: 0.7759 (tmm) REVERT: A 597 ASP cc_start: 0.7782 (t0) cc_final: 0.7350 (t0) REVERT: A 600 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8255 (mttm) REVERT: E 506 GLN cc_start: 0.8926 (mt0) cc_final: 0.8627 (mt0) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 0.1615 time to fit residues: 27.3601 Evaluate side-chains 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 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 47 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.176243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.149479 restraints weight = 9533.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.151168 restraints weight = 13879.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.152798 restraints weight = 10579.864| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6668 Z= 0.168 Angle : 0.548 8.369 9064 Z= 0.278 Chirality : 0.043 0.205 961 Planarity : 0.004 0.039 1171 Dihedral : 4.658 38.633 967 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.73 % Allowed : 14.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 788 helix: 0.23 (0.26), residues: 396 sheet: 0.25 (0.69), residues: 47 loop : 0.17 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 594 HIS 0.004 0.001 HIS A 535 PHE 0.027 0.002 PHE A 308 TYR 0.014 0.001 TYR E 495 ARG 0.004 0.000 ARG A 161 *********************** 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 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8118 (tp30) cc_final: 0.7728 (tp30) REVERT: A 57 GLU cc_start: 0.7610 (tp30) cc_final: 0.7252 (tm-30) REVERT: A 123 MET cc_start: 0.6288 (mtt) cc_final: 0.5836 (mtt) REVERT: A 127 TYR cc_start: 0.8079 (t80) cc_final: 0.7857 (t80) REVERT: A 207 TYR cc_start: 0.8246 (m-80) cc_final: 0.7515 (m-10) REVERT: A 219 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: A 360 MET cc_start: 0.6390 (tmm) cc_final: 0.5732 (ttm) REVERT: A 366 MET cc_start: 0.8351 (tmm) cc_final: 0.7930 (tmm) REVERT: E 346 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7196 (ptp-110) REVERT: E 444 LYS cc_start: 0.8798 (mttm) cc_final: 0.8466 (pttt) outliers start: 11 outliers final: 11 residues processed: 108 average time/residue: 0.1658 time to fit residues: 25.0772 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 365 THR Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.174299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.147046 restraints weight = 10148.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.145248 restraints weight = 11689.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.147860 restraints weight = 10309.928| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 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 = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6668 Z= 0.174 Angle : 0.535 8.416 9064 Z= 0.272 Chirality : 0.043 0.196 961 Planarity : 0.004 0.037 1171 Dihedral : 4.426 33.892 967 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.45 % Allowed : 14.24 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.29), residues: 788 helix: 0.52 (0.26), residues: 394 sheet: -0.03 (0.70), residues: 47 loop : 0.20 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 302 HIS 0.004 0.001 HIS A 535 PHE 0.018 0.001 PHE A 308 TYR 0.012 0.001 TYR E 495 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8337 (tp30) cc_final: 0.7877 (tp30) REVERT: A 57 GLU cc_start: 0.7832 (tp30) cc_final: 0.7359 (tm-30) REVERT: A 123 MET cc_start: 0.6354 (mtt) cc_final: 0.5968 (mtt) REVERT: A 174 LYS cc_start: 0.7599 (mmtp) cc_final: 0.7321 (mmtm) REVERT: A 219 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7766 (mtm-85) REVERT: A 259 ILE cc_start: 0.8490 (pt) cc_final: 0.8167 (mt) REVERT: A 360 MET cc_start: 0.6648 (tmm) cc_final: 0.6337 (ttm) REVERT: A 366 MET cc_start: 0.8327 (tmm) cc_final: 0.7833 (tmm) REVERT: A 410 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7680 (mp) REVERT: E 444 LYS cc_start: 0.8979 (mttm) cc_final: 0.8400 (pttt) outliers start: 16 outliers final: 13 residues processed: 110 average time/residue: 0.1558 time to fit residues: 24.1043 Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 152 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 519 HIS Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3811 r_free = 0.3811 target = 0.172381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.150299 restraints weight = 11955.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.148020 restraints weight = 17078.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.146973 restraints weight = 7856.077| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6668 Z= 0.210 Angle : 0.547 8.801 9064 Z= 0.282 Chirality : 0.044 0.143 961 Planarity : 0.004 0.039 1171 Dihedral : 4.458 30.979 967 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.01 % Allowed : 15.40 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.29), residues: 788 helix: 0.64 (0.26), residues: 394 sheet: -0.28 (0.70), residues: 49 loop : 0.14 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 478 HIS 0.005 0.001 HIS A 535 PHE 0.016 0.002 PHE A 356 TYR 0.012 0.001 TYR E 396 ARG 0.004 0.000 ARG A 161 *********************** 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 118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8267 (tp30) cc_final: 0.7892 (tm-30) REVERT: A 57 GLU cc_start: 0.7898 (tp30) cc_final: 0.7435 (tm-30) REVERT: A 123 MET cc_start: 0.6380 (mtt) cc_final: 0.5915 (mtt) REVERT: A 174 LYS cc_start: 0.7686 (mmtp) cc_final: 0.7410 (mmtm) REVERT: A 219 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7760 (mtm-85) REVERT: A 222 LEU cc_start: 0.7888 (tp) cc_final: 0.7677 (tp) REVERT: A 259 ILE cc_start: 0.8412 (pt) cc_final: 0.8127 (mt) REVERT: A 349 TRP cc_start: 0.8639 (m100) cc_final: 0.8149 (m100) REVERT: A 360 MET cc_start: 0.6868 (tmm) cc_final: 0.6391 (ttm) outliers start: 13 outliers final: 11 residues processed: 112 average time/residue: 0.1530 time to fit residues: 24.2004 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 0.0040 chunk 13 optimal weight: 0.0470 chunk 72 optimal weight: 0.3980 chunk 32 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.1288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.176145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.149904 restraints weight = 9565.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.150095 restraints weight = 13424.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.153447 restraints weight = 10121.941| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6668 Z= 0.125 Angle : 0.497 8.536 9064 Z= 0.252 Chirality : 0.040 0.144 961 Planarity : 0.004 0.036 1171 Dihedral : 4.098 30.862 967 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.44 % Allowed : 16.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 788 helix: 0.97 (0.26), residues: 396 sheet: -0.09 (0.74), residues: 47 loop : 0.26 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 478 HIS 0.004 0.001 HIS A 535 PHE 0.018 0.001 PHE A 504 TYR 0.008 0.001 TYR E 508 ARG 0.003 0.000 ARG A 161 *********************** 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 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.680 Fit side-chains REVERT: A 35 GLU cc_start: 0.8267 (tp30) cc_final: 0.7649 (tp30) REVERT: A 57 GLU cc_start: 0.7727 (tp30) cc_final: 0.7377 (tm-30) REVERT: A 123 MET cc_start: 0.6239 (mtt) cc_final: 0.5912 (mtt) REVERT: A 207 TYR cc_start: 0.7897 (m-80) cc_final: 0.7433 (m-10) REVERT: A 259 ILE cc_start: 0.8302 (pt) cc_final: 0.8051 (mt) REVERT: A 323 MET cc_start: 0.8058 (mmm) cc_final: 0.7509 (mmm) REVERT: A 353 LYS cc_start: 0.8807 (mttt) cc_final: 0.8323 (mtpt) REVERT: A 360 MET cc_start: 0.6497 (tmm) cc_final: 0.5975 (ttm) REVERT: A 366 MET cc_start: 0.8539 (tmm) cc_final: 0.8325 (tmm) REVERT: A 385 TYR cc_start: 0.8717 (p90) cc_final: 0.8493 (p90) outliers start: 9 outliers final: 8 residues processed: 104 average time/residue: 0.1585 time to fit residues: 23.3849 Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 365 THR Chi-restraints excluded: chain E residue 334 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 439 ASN E 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.171640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155636 restraints weight = 10159.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.151907 restraints weight = 14144.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.148350 restraints weight = 10113.391| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6668 Z= 0.176 Angle : 0.521 8.718 9064 Z= 0.267 Chirality : 0.042 0.158 961 Planarity : 0.004 0.036 1171 Dihedral : 4.113 29.345 967 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.73 % Allowed : 16.98 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 788 helix: 0.99 (0.27), residues: 394 sheet: -0.08 (0.75), residues: 47 loop : 0.22 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 478 HIS 0.004 0.001 HIS A 535 PHE 0.016 0.002 PHE A 315 TYR 0.010 0.001 TYR E 508 ARG 0.004 0.000 ARG A 161 *********************** 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 120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8214 (tp30) cc_final: 0.7687 (tp30) REVERT: A 57 GLU cc_start: 0.7828 (tp30) cc_final: 0.7484 (tm-30) REVERT: A 123 MET cc_start: 0.6228 (mtt) cc_final: 0.5841 (mtt) REVERT: A 259 ILE cc_start: 0.8299 (pt) cc_final: 0.8055 (mt) REVERT: A 349 TRP cc_start: 0.8621 (m100) cc_final: 0.8091 (m100) REVERT: A 353 LYS cc_start: 0.8882 (mttt) cc_final: 0.8517 (mtpt) REVERT: A 360 MET cc_start: 0.6644 (tmm) cc_final: 0.6146 (ttm) REVERT: A 366 MET cc_start: 0.8581 (tmm) cc_final: 0.8347 (tmm) REVERT: A 383 MET cc_start: 0.8412 (mtm) cc_final: 0.8146 (mtt) REVERT: A 515 TYR cc_start: 0.7790 (m-10) cc_final: 0.7498 (m-10) outliers start: 11 outliers final: 11 residues processed: 116 average time/residue: 0.1548 time to fit residues: 25.3767 Evaluate side-chains 114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 365 THR Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 439 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.169785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.154850 restraints weight = 18980.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.150658 restraints weight = 22693.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.147483 restraints weight = 11170.368| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6668 Z= 0.219 Angle : 0.556 8.784 9064 Z= 0.288 Chirality : 0.044 0.172 961 Planarity : 0.004 0.036 1171 Dihedral : 4.288 31.373 967 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.87 % Allowed : 17.41 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 788 helix: 0.85 (0.26), residues: 400 sheet: -0.02 (0.76), residues: 47 loop : 0.25 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 478 HIS 0.005 0.001 HIS A 535 PHE 0.014 0.002 PHE E 429 TYR 0.015 0.001 TYR E 508 ARG 0.004 0.001 ARG A 161 *********************** 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 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8350 (tp30) cc_final: 0.7956 (tm-30) REVERT: A 57 GLU cc_start: 0.7931 (tp30) cc_final: 0.7517 (tm-30) REVERT: A 123 MET cc_start: 0.6371 (mtt) cc_final: 0.5959 (mtt) REVERT: A 207 TYR cc_start: 0.8280 (m-80) cc_final: 0.7649 (m-10) REVERT: A 349 TRP cc_start: 0.8708 (m100) cc_final: 0.8206 (m100) REVERT: A 353 LYS cc_start: 0.8885 (mttt) cc_final: 0.8526 (mtpt) REVERT: A 360 MET cc_start: 0.6791 (tmm) cc_final: 0.6277 (ttm) REVERT: A 366 MET cc_start: 0.8645 (tmm) cc_final: 0.8407 (tmm) outliers start: 12 outliers final: 10 residues processed: 111 average time/residue: 0.1606 time to fit residues: 25.0841 Evaluate side-chains 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 55 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3814 r_free = 0.3814 target = 0.171562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.153835 restraints weight = 9819.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.151160 restraints weight = 13869.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.152264 restraints weight = 12712.720| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6668 Z= 0.187 Angle : 0.541 8.629 9064 Z= 0.280 Chirality : 0.042 0.171 961 Planarity : 0.004 0.035 1171 Dihedral : 4.238 32.305 967 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.44 % Allowed : 17.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 788 helix: 0.87 (0.26), residues: 400 sheet: -0.00 (0.77), residues: 47 loop : 0.25 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 478 HIS 0.005 0.001 HIS A 535 PHE 0.014 0.001 PHE A 356 TYR 0.010 0.001 TYR E 508 ARG 0.004 0.000 ARG A 161 ********************** 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8026 (tp30) cc_final: 0.7699 (tp30) REVERT: A 57 GLU cc_start: 0.7595 (tp30) cc_final: 0.7342 (tm-30) REVERT: A 123 MET cc_start: 0.6051 (mtt) cc_final: 0.5690 (mtt) REVERT: A 207 TYR cc_start: 0.8295 (m-80) cc_final: 0.7708 (m-10) REVERT: A 349 TRP cc_start: 0.8551 (m100) cc_final: 0.8066 (m100) REVERT: A 353 LYS cc_start: 0.8857 (mttt) cc_final: 0.8607 (mtpt) outliers start: 9 outliers final: 9 residues processed: 108 average time/residue: 0.1542 time to fit residues: 23.3317 Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain E residue 334 ASN 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 73 optimal weight: 0.5980 chunk 59 optimal weight: 0.0980 chunk 76 optimal weight: 0.1980 chunk 18 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.0370 chunk 61 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 47 optimal weight: 3.9990 overall best weight: 0.1656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3827 r_free = 0.3827 target = 0.174695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.146998 restraints weight = 11531.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.150462 restraints weight = 16595.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.152657 restraints weight = 8180.707| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6668 Z= 0.145 Angle : 0.540 9.213 9064 Z= 0.274 Chirality : 0.041 0.148 961 Planarity : 0.004 0.035 1171 Dihedral : 4.091 32.303 967 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.15 % Allowed : 17.99 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.30), residues: 788 helix: 1.00 (0.26), residues: 400 sheet: -0.16 (0.77), residues: 47 loop : 0.26 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 478 HIS 0.004 0.001 HIS A 535 PHE 0.019 0.001 PHE A 504 TYR 0.014 0.001 TYR A 515 ARG 0.003 0.000 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2452.15 seconds wall clock time: 44 minutes 36.05 seconds (2676.05 seconds total)