Starting phenix.real_space_refine on Tue Mar 11 19:35:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vx5_32169/03_2025/7vx5_32169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx5_32169/03_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_32169/03_2025/7vx5_32169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx5_32169/03_2025/7vx5_32169.map" model { file = "/net/cci-nas-00/data/ceres_data/7vx5_32169/03_2025/7vx5_32169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx5_32169/03_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-5624/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: 7.07, per 1000 atoms: 1.09 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: 1.58 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: 0.72 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: 1.66 Time building geometry restraints manager: 1.89 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.280 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.750 ------------------------------------------------------------------------------- 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 : 0.741 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: 0.1914 time to fit residues: 51.0185 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 : 0.640 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.160915 restraints weight = 15584.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.163217 restraints weight = 18116.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.164708 restraints weight = 6921.173| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 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 = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 9.609 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 : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7183 (m-30) cc_final: 0.6965 (t0) REVERT: A 194 ASN cc_start: 0.7002 (OUTLIER) cc_final: 0.6681 (t0) REVERT: A 207 TYR cc_start: 0.8235 (m-80) cc_final: 0.7529 (m-10) REVERT: A 217 TYR cc_start: 0.8091 (t80) cc_final: 0.7656 (t80) REVERT: A 219 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7357 (mtm-85) REVERT: A 270 MET cc_start: 0.3179 (tpp) cc_final: 0.2563 (tpp) REVERT: A 360 MET cc_start: 0.6489 (tmm) cc_final: 0.6059 (ttm) REVERT: A 366 MET cc_start: 0.8224 (tmm) cc_final: 0.7660 (tmm) REVERT: E 347 PHE cc_start: 0.8259 (m-10) cc_final: 0.8018 (m-80) outliers start: 9 outliers final: 8 residues processed: 144 average time/residue: 0.1648 time to fit residues: 33.1945 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 : 0.734 ------------------------------------------------------------------------------- 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: 0.3980 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 62 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 37 optimal weight: 0.8980 overall best weight: 0.2814 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.181154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.153723 restraints weight = 11207.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.158058 restraints weight = 15212.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.158895 restraints weight = 9004.542| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3924 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= 0.167 Angle : 0.563 7.859 9064 Z= 0.289 Chirality : 0.043 0.182 961 Planarity : 0.004 0.036 1171 Dihedral : 4.962 39.841 967 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.73 % Allowed : 13.53 % Favored : 84.75 % 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: -0.13 (0.28), residues: 788 helix: -0.14 (0.25), residues: 395 sheet: 0.34 (0.69), residues: 46 loop : 0.16 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 594 HIS 0.004 0.001 HIS A 378 PHE 0.019 0.002 PHE A 308 TYR 0.019 0.001 TYR E 495 ARG 0.004 0.000 ARG A 169 *********************** 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 132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7737 (tp30) cc_final: 0.7330 (tm-30) REVERT: A 160 GLU cc_start: 0.7681 (tp30) cc_final: 0.7318 (tp30) REVERT: A 194 ASN cc_start: 0.6921 (OUTLIER) cc_final: 0.6692 (t0) REVERT: A 207 TYR cc_start: 0.8147 (m-80) cc_final: 0.7468 (m-10) REVERT: A 219 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7313 (mtm-85) REVERT: A 360 MET cc_start: 0.6267 (tmm) cc_final: 0.5674 (ttm) REVERT: A 366 MET cc_start: 0.8308 (tmm) cc_final: 0.7764 (tmm) REVERT: A 597 ASP cc_start: 0.7403 (t0) cc_final: 0.7005 (t0) outliers start: 12 outliers final: 7 residues processed: 127 average time/residue: 0.1569 time to fit residues: 28.3972 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 194 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: 2.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.170693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.145456 restraints weight = 10042.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.146154 restraints weight = 12436.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.147632 restraints weight = 10388.405| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 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 = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6668 Z= 0.231 Angle : 0.593 7.826 9064 Z= 0.303 Chirality : 0.045 0.216 961 Planarity : 0.004 0.038 1171 Dihedral : 4.805 38.910 967 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.45 % Allowed : 14.68 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.29), residues: 788 helix: 0.19 (0.26), residues: 395 sheet: 0.14 (0.67), residues: 49 loop : 0.18 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 594 HIS 0.004 0.001 HIS A 535 PHE 0.027 0.002 PHE A 308 TYR 0.017 0.002 TYR E 495 ARG 0.005 0.001 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 121 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8313 (tp30) cc_final: 0.7821 (tp30) REVERT: A 57 GLU cc_start: 0.7685 (tp30) cc_final: 0.7237 (tm-30) REVERT: A 123 MET cc_start: 0.6363 (mtt) cc_final: 0.5931 (mtt) REVERT: A 127 TYR cc_start: 0.8174 (t80) cc_final: 0.7953 (t80) REVERT: A 194 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6881 (t0) REVERT: A 349 TRP cc_start: 0.8692 (m100) cc_final: 0.8351 (m100) REVERT: A 360 MET cc_start: 0.6393 (tmm) cc_final: 0.5942 (ttm) REVERT: A 366 MET cc_start: 0.8403 (tmm) cc_final: 0.7871 (tmm) outliers start: 17 outliers final: 13 residues processed: 115 average time/residue: 0.1789 time to fit residues: 29.2417 Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 194 ASN Chi-restraints excluded: chain A residue 365 THR 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 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: 0.7980 chunk 44 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.174167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.147082 restraints weight = 10124.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.146559 restraints weight = 10830.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.148666 restraints weight = 9095.986| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 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 = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6668 Z= 0.189 Angle : 0.553 8.795 9064 Z= 0.282 Chirality : 0.043 0.142 961 Planarity : 0.004 0.036 1171 Dihedral : 4.586 35.048 967 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.16 % Allowed : 14.96 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.29), residues: 788 helix: 0.45 (0.26), residues: 395 sheet: 0.02 (0.71), residues: 47 loop : 0.14 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 478 HIS 0.004 0.001 HIS A 535 PHE 0.013 0.002 PHE E 497 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 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8209 (tp30) cc_final: 0.7768 (tp30) REVERT: A 57 GLU cc_start: 0.7844 (tp30) cc_final: 0.7378 (tm-30) REVERT: A 123 MET cc_start: 0.6357 (mtt) cc_final: 0.5979 (mtt) REVERT: A 360 MET cc_start: 0.6622 (tmm) cc_final: 0.6332 (ttm) REVERT: A 366 MET cc_start: 0.8393 (tmm) cc_final: 0.7882 (tmm) REVERT: E 506 GLN cc_start: 0.8292 (mt0) cc_final: 0.8079 (mt0) outliers start: 14 outliers final: 13 residues processed: 102 average time/residue: 0.1602 time to fit residues: 22.9742 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 411 SER 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: 0.1980 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.175104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.148205 restraints weight = 11965.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.152779 restraints weight = 17253.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.153682 restraints weight = 6804.701| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6668 Z= 0.169 Angle : 0.529 8.410 9064 Z= 0.269 Chirality : 0.042 0.139 961 Planarity : 0.004 0.038 1171 Dihedral : 4.388 30.621 967 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.87 % Allowed : 15.11 % Favored : 83.02 % 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: 0.56 (0.29), residues: 788 helix: 0.78 (0.27), residues: 395 sheet: -0.11 (0.72), residues: 47 loop : 0.14 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 478 HIS 0.005 0.001 HIS A 535 PHE 0.011 0.001 PHE E 497 TYR 0.010 0.001 TYR E 495 ARG 0.003 0.000 ARG A 219 *********************** 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: 12 poor density : 100 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8323 (tp30) cc_final: 0.7711 (tp30) REVERT: A 57 GLU cc_start: 0.7820 (tp30) cc_final: 0.7397 (tm-30) REVERT: A 123 MET cc_start: 0.6366 (mtt) cc_final: 0.6025 (mtt) REVERT: A 259 ILE cc_start: 0.8392 (pt) cc_final: 0.8095 (mt) REVERT: A 360 MET cc_start: 0.6714 (tmm) cc_final: 0.6197 (ttm) outliers start: 12 outliers final: 10 residues processed: 106 average time/residue: 0.1538 time to fit residues: 23.2681 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 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: 1.9990 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 0.0170 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** E 439 ASN ** 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 = 0.3824 r_free = 0.3824 target = 0.172629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.155662 restraints weight = 9798.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.155061 restraints weight = 13133.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.154302 restraints weight = 8853.929| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 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 = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6668 Z= 0.169 Angle : 0.530 8.552 9064 Z= 0.271 Chirality : 0.042 0.147 961 Planarity : 0.004 0.037 1171 Dihedral : 4.281 30.397 967 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.58 % Allowed : 16.69 % 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 (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: 0.67 (0.30), residues: 788 helix: 0.84 (0.26), residues: 399 sheet: -0.08 (0.76), residues: 47 loop : 0.22 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 302 HIS 0.005 0.001 HIS A 535 PHE 0.016 0.001 PHE A 356 TYR 0.013 0.001 TYR E 380 ARG 0.004 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 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8142 (tp30) cc_final: 0.7582 (tp30) REVERT: A 57 GLU cc_start: 0.7718 (tp30) cc_final: 0.7432 (tm-30) REVERT: A 123 MET cc_start: 0.6265 (mtt) cc_final: 0.5922 (mtt) REVERT: A 259 ILE cc_start: 0.8135 (pt) cc_final: 0.7886 (mt) REVERT: A 349 TRP cc_start: 0.8611 (m100) cc_final: 0.8065 (m100) REVERT: A 360 MET cc_start: 0.6416 (tmm) cc_final: 0.5770 (ttm) REVERT: A 366 MET cc_start: 0.8570 (tmm) cc_final: 0.8321 (tmm) REVERT: E 489 TYR cc_start: 0.7515 (m-80) cc_final: 0.7237 (m-80) outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.1509 time to fit residues: 22.0583 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 469 SER 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: 0.8980 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.168478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.150313 restraints weight = 10249.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.149561 restraints weight = 15609.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.147234 restraints weight = 9233.222| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 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 = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6668 Z= 0.228 Angle : 0.563 8.407 9064 Z= 0.290 Chirality : 0.044 0.164 961 Planarity : 0.004 0.037 1171 Dihedral : 4.459 32.056 967 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.73 % Allowed : 16.83 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.30), residues: 788 helix: 0.78 (0.26), residues: 399 sheet: -0.17 (0.74), residues: 49 loop : 0.18 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 302 HIS 0.005 0.001 HIS A 535 PHE 0.015 0.002 PHE E 429 TYR 0.012 0.001 TYR E 453 ARG 0.004 0.001 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 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8333 (tp30) cc_final: 0.7944 (tm-30) REVERT: A 57 GLU cc_start: 0.7854 (tp30) cc_final: 0.7474 (tm-30) REVERT: A 123 MET cc_start: 0.6391 (mtt) cc_final: 0.6025 (mtt) REVERT: A 349 TRP cc_start: 0.8661 (m100) cc_final: 0.8196 (m100) REVERT: A 353 LYS cc_start: 0.8954 (mttt) cc_final: 0.8479 (mtpt) REVERT: A 360 MET cc_start: 0.6753 (tmm) cc_final: 0.6209 (ttm) REVERT: A 366 MET cc_start: 0.8680 (tmm) cc_final: 0.8406 (tmm) REVERT: E 489 TYR cc_start: 0.7584 (m-80) cc_final: 0.7277 (m-80) outliers start: 11 outliers final: 9 residues processed: 102 average time/residue: 0.1718 time to fit residues: 24.8583 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 469 SER 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: 0.1980 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.182355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.163833 restraints weight = 18879.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.162873 restraints weight = 22959.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.161774 restraints weight = 8641.994| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6668 Z= 0.214 Angle : 0.554 8.136 9064 Z= 0.286 Chirality : 0.043 0.165 961 Planarity : 0.004 0.035 1171 Dihedral : 4.419 33.873 967 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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 (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: 0.62 (0.30), residues: 788 helix: 0.88 (0.27), residues: 393 sheet: -0.02 (0.77), residues: 47 loop : 0.09 (0.33), residues: 348 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 0.024 0.002 PHE A 356 TYR 0.011 0.001 TYR E 453 ARG 0.004 0.000 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8263 (tp30) cc_final: 0.7948 (tm-30) REVERT: A 57 GLU cc_start: 0.7876 (tp30) cc_final: 0.7461 (tm-30) REVERT: A 123 MET cc_start: 0.6257 (mtt) cc_final: 0.5889 (mtt) REVERT: A 270 MET cc_start: 0.4751 (tpt) cc_final: 0.4445 (tpp) REVERT: A 349 TRP cc_start: 0.8682 (m100) cc_final: 0.8162 (m100) REVERT: A 353 LYS cc_start: 0.8949 (mttt) cc_final: 0.8621 (mtpt) REVERT: A 366 MET cc_start: 0.8651 (tmm) cc_final: 0.8394 (tmm) REVERT: E 489 TYR cc_start: 0.7564 (m-80) cc_final: 0.7260 (m-80) outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 0.1626 time to fit residues: 24.4173 Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 411 SER Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 387 LEU 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: 0.9980 chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 58 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.173579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.149338 restraints weight = 9749.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.150199 restraints weight = 12722.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.152092 restraints weight = 9711.057| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6668 Z= 0.192 Angle : 0.562 8.262 9064 Z= 0.287 Chirality : 0.043 0.176 961 Planarity : 0.004 0.035 1171 Dihedral : 4.377 33.874 967 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.87 % Allowed : 16.40 % 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 (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: 0.65 (0.30), residues: 788 helix: 0.92 (0.27), residues: 393 sheet: -0.13 (0.77), residues: 47 loop : 0.10 (0.33), residues: 348 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 0.012 0.001 PHE E 429 TYR 0.015 0.001 TYR A 515 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 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8305 (tp30) cc_final: 0.7948 (tm-30) REVERT: A 57 GLU cc_start: 0.7749 (tp30) cc_final: 0.7397 (tm-30) REVERT: A 123 MET cc_start: 0.6284 (mtt) cc_final: 0.5924 (mtt) REVERT: A 270 MET cc_start: 0.4709 (tpt) cc_final: 0.4479 (tpp) REVERT: A 349 TRP cc_start: 0.8634 (m100) cc_final: 0.8144 (m100) REVERT: A 353 LYS cc_start: 0.8980 (mttt) cc_final: 0.8583 (mtpt) REVERT: A 366 MET cc_start: 0.8656 (tmm) cc_final: 0.8412 (tmm) REVERT: E 489 TYR cc_start: 0.7550 (m-80) cc_final: 0.7240 (m-80) outliers start: 12 outliers final: 11 residues processed: 110 average time/residue: 0.1480 time to fit residues: 22.9594 Evaluate side-chains 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 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 411 SER Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 387 LEU 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: 0.2980 chunk 59 optimal weight: 0.0870 chunk 76 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.0270 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.177171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.150661 restraints weight = 11867.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.151743 restraints weight = 16229.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.153462 restraints weight = 10859.637| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6668 Z= 0.150 Angle : 0.561 11.197 9064 Z= 0.281 Chirality : 0.042 0.161 961 Planarity : 0.004 0.035 1171 Dihedral : 4.238 33.643 967 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.73 % Allowed : 17.12 % 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: 0.77 (0.30), residues: 788 helix: 1.02 (0.27), residues: 393 sheet: -0.19 (0.77), residues: 47 loop : 0.18 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 478 HIS 0.005 0.001 HIS A 505 PHE 0.033 0.001 PHE A 327 TYR 0.017 0.001 TYR E 380 ARG 0.003 0.000 ARG A 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.93 seconds wall clock time: 46 minutes 27.70 seconds (2787.70 seconds total)