Starting phenix.real_space_refine on Tue Mar 11 17:12:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9i_32367/03_2025/7w9i_32367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9i_32367/03_2025/7w9i_32367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w9i_32367/03_2025/7w9i_32367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9i_32367/03_2025/7w9i_32367.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9i_32367/03_2025/7w9i_32367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9i_32367/03_2025/7w9i_32367.cif" } resolution = 3.4 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= -0.000 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4101 2.51 5 N 1066 2.21 5 O 1208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 6412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Time building chain proxies: 5.00, per 1000 atoms: 0.78 Number of scatterers: 6412 At special positions: 0 Unit cell: (91.812, 84.161, 119.137, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1208 8.00 N 1066 7.00 C 4101 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=2.04 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 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 903.4 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 48.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 removed outlier: 3.711A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 53 removed outlier: 3.577A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 removed outlier: 3.667A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.655A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.122A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.552A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.508A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 152' Processing helix chain 'A' and resid 158 through 167 removed outlier: 3.831A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.923A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.683A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 248 removed outlier: 3.589A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.829A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (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 279 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.607A pdb=" N MET A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 4.188A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.979A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 331' Processing helix chain 'A' and resid 368 through 378 removed outlier: 3.609A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.536A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.668A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.720A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.700A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.650A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.040A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (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 512 through 515 Processing helix chain 'A' and resid 516 through 533 removed outlier: 3.671A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.668A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.696A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.925A 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 598 removed outlier: 3.623A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.001A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.766A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.897A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 385 through 389' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.621A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.530A pdb=" N TYR E 505 " --> pdb=" O GLY E 502 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 506' Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.638A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.409A 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: 6.200A 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: 3.528A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (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 474 197 hydrogen bonds defined for protein. 543 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: 1.88 Time building geometry restraints manager: 1.82 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: 2065 1.34 - 1.46: 1673 1.46 - 1.58: 2796 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6592 Sorted by residual: bond pdb=" C VAL A 488 " pdb=" N GLU A 489 " ideal model delta sigma weight residual 1.331 1.279 0.052 2.07e-02 2.33e+03 6.20e+00 bond pdb=" C LYS E 478 " pdb=" N PRO E 479 " ideal model delta sigma weight residual 1.338 1.364 -0.026 1.90e-02 2.77e+03 1.80e+00 bond pdb=" C ARG A 177 " pdb=" N PRO A 178 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.25e-02 6.40e+03 1.49e+00 bond pdb=" C ASP A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.25e-02 6.40e+03 1.44e+00 bond pdb=" CB VAL A 581 " pdb=" CG2 VAL A 581 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.43e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 8819 2.36 - 4.71: 118 4.71 - 7.07: 13 7.07 - 9.43: 6 9.43 - 11.79: 2 Bond angle restraints: 8958 Sorted by residual: angle pdb=" C LYS E 478 " pdb=" N PRO E 479 " pdb=" CA PRO E 479 " ideal model delta sigma weight residual 127.00 138.79 -11.79 2.40e+00 1.74e-01 2.41e+01 angle pdb=" C LYS E 478 " pdb=" N PRO E 479 " pdb=" CD PRO E 479 " ideal model delta sigma weight residual 120.60 111.48 9.12 2.20e+00 2.07e-01 1.72e+01 angle pdb=" N ARG A 582 " pdb=" CA ARG A 582 " pdb=" C ARG A 582 " ideal model delta sigma weight residual 109.81 117.59 -7.78 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N ASP A 499 " pdb=" CA ASP A 499 " pdb=" C ASP A 499 " ideal model delta sigma weight residual 109.81 116.86 -7.05 2.21e+00 2.05e-01 1.02e+01 angle pdb=" CA LEU A 143 " pdb=" CB LEU A 143 " pdb=" CG LEU A 143 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.13e+00 ... (remaining 8953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3450 17.85 - 35.71: 365 35.71 - 53.56: 58 53.56 - 71.41: 15 71.41 - 89.27: 5 Dihedral angle restraints: 3893 sinusoidal: 1573 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 134.75 -41.75 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA LEU E 461 " pdb=" C LEU E 461 " pdb=" N LYS E 462 " pdb=" CA LYS E 462 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 744 0.056 - 0.111: 166 0.111 - 0.167: 22 0.167 - 0.222: 1 0.222 - 0.278: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" CB ILE A 291 " pdb=" CA ILE A 291 " pdb=" CG1 ILE A 291 " pdb=" CG2 ILE A 291 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL A 364 " pdb=" CA VAL A 364 " pdb=" CG1 VAL A 364 " pdb=" CG2 VAL A 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.80 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB VAL E 350 " pdb=" CA VAL E 350 " pdb=" CG1 VAL E 350 " pdb=" CG2 VAL E 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 931 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.044 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 583 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 235 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 520 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO E 521 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 521 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 521 " 0.033 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1967 2.81 - 3.33: 5129 3.33 - 3.86: 10439 3.86 - 4.38: 12633 4.38 - 4.90: 21601 Nonbonded interactions: 51769 Sorted by model distance: nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.289 3.040 nonbonded pdb=" OD1 ASP A 543 " pdb=" OG SER A 545 " model vdw 2.319 3.040 nonbonded pdb=" OG SER A 170 " pdb=" OE1 GLU A 171 " model vdw 2.344 3.040 nonbonded pdb=" OG SER E 371 " pdb=" OG SER E 373 " model vdw 2.348 3.040 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.360 3.040 ... (remaining 51764 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.840 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.005 0.052 6592 Z= 0.292 Angle : 0.724 11.787 8958 Z= 0.382 Chirality : 0.049 0.278 934 Planarity : 0.006 0.065 1165 Dihedral : 14.898 89.268 2384 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -5.48 (0.21), residues: 787 helix: -4.83 (0.08), residues: 351 sheet: -2.24 (0.72), residues: 49 loop : -2.53 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.004 0.001 HIS E 519 PHE 0.015 0.002 PHE A 452 TYR 0.025 0.002 TYR E 453 ARG 0.007 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 50 TYR cc_start: 0.8635 (t80) cc_final: 0.8433 (t80) REVERT: A 62 MET cc_start: 0.7878 (ptm) cc_final: 0.7601 (ptm) REVERT: A 255 TYR cc_start: 0.7287 (m-80) cc_final: 0.7075 (m-10) REVERT: A 375 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 398 GLU cc_start: 0.8189 (pt0) cc_final: 0.7875 (pt0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2489 time to fit residues: 40.3752 Evaluate side-chains 86 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 0.7980 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.0040 chunk 45 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 58 ASN A 81 GLN A 89 GLN A 96 GLN A 103 ASN A 373 HIS A 378 HIS E 474 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152926 restraints weight = 7915.386| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.11 r_work: 0.3503 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6592 Z= 0.176 Angle : 0.517 7.249 8958 Z= 0.262 Chirality : 0.042 0.156 934 Planarity : 0.005 0.044 1165 Dihedral : 4.375 17.247 861 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.30 % Allowed : 11.10 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -3.85 (0.25), residues: 787 helix: -3.21 (0.19), residues: 354 sheet: -1.55 (0.72), residues: 47 loop : -1.92 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.003 0.001 HIS A 505 PHE 0.014 0.001 PHE E 377 TYR 0.018 0.001 TYR A 202 ARG 0.004 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8090 (tmm) cc_final: 0.7884 (tmm) REVERT: A 255 TYR cc_start: 0.7578 (m-80) cc_final: 0.7301 (m-10) REVERT: A 332 MET cc_start: 0.8558 (ttp) cc_final: 0.7454 (ttp) REVERT: A 375 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7252 (mm-30) REVERT: A 398 GLU cc_start: 0.8430 (pt0) cc_final: 0.8169 (pt0) REVERT: A 479 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 452 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.8169 (mtm180) REVERT: E 508 TYR cc_start: 0.8484 (m-80) cc_final: 0.7828 (m-80) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.1543 time to fit residues: 23.3458 Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 ASN 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 25 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 0.0060 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.185355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153297 restraints weight = 7996.126| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.08 r_work: 0.3479 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6592 Z= 0.161 Angle : 0.489 7.192 8958 Z= 0.243 Chirality : 0.042 0.146 934 Planarity : 0.004 0.036 1165 Dihedral : 3.992 15.438 861 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.59 % Allowed : 12.82 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.77 (0.27), residues: 787 helix: -2.05 (0.24), residues: 352 sheet: -1.69 (0.66), residues: 50 loop : -1.53 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.002 0.000 HIS E 519 PHE 0.011 0.001 PHE E 377 TYR 0.018 0.001 TYR A 202 ARG 0.006 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.711 Fit side-chains REVERT: A 157 ASP cc_start: 0.7338 (t0) cc_final: 0.7064 (t0) REVERT: A 255 TYR cc_start: 0.7600 (m-80) cc_final: 0.7375 (m-10) REVERT: A 332 MET cc_start: 0.8642 (ttp) cc_final: 0.7512 (ttp) REVERT: A 375 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 398 GLU cc_start: 0.8431 (pt0) cc_final: 0.8156 (pt0) REVERT: A 479 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7493 (tm-30) REVERT: E 508 TYR cc_start: 0.8447 (m-80) cc_final: 0.7814 (m-80) outliers start: 11 outliers final: 9 residues processed: 99 average time/residue: 0.1632 time to fit residues: 22.6576 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.179210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147261 restraints weight = 7887.553| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.05 r_work: 0.3455 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6592 Z= 0.208 Angle : 0.502 7.198 8958 Z= 0.246 Chirality : 0.042 0.118 934 Planarity : 0.003 0.034 1165 Dihedral : 4.002 16.187 861 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.59 % Allowed : 14.41 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.28 (0.28), residues: 787 helix: -1.56 (0.26), residues: 358 sheet: -1.02 (0.69), residues: 47 loop : -1.42 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 PHE 0.013 0.001 PHE A 369 TYR 0.016 0.001 TYR E 453 ARG 0.006 0.001 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.761 Fit side-chains REVERT: A 157 ASP cc_start: 0.7317 (t0) cc_final: 0.7018 (t0) REVERT: A 255 TYR cc_start: 0.7564 (m-80) cc_final: 0.7359 (m-10) REVERT: A 332 MET cc_start: 0.8669 (ttp) cc_final: 0.7503 (ttp) REVERT: A 375 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7433 (mm-30) REVERT: A 398 GLU cc_start: 0.8554 (pt0) cc_final: 0.8226 (pt0) REVERT: A 479 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7432 (tm-30) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 0.1657 time to fit residues: 22.4735 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 42 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.186155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154111 restraints weight = 7939.562| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.07 r_work: 0.3489 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6592 Z= 0.134 Angle : 0.476 7.731 8958 Z= 0.230 Chirality : 0.041 0.120 934 Planarity : 0.003 0.037 1165 Dihedral : 3.748 13.949 861 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.87 % Allowed : 14.99 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.79 (0.29), residues: 787 helix: -1.11 (0.27), residues: 359 sheet: -1.24 (0.69), residues: 49 loop : -1.12 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.002 0.001 HIS A 505 PHE 0.007 0.001 PHE A 369 TYR 0.021 0.001 TYR A 202 ARG 0.004 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 119 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6687 (tp) REVERT: A 157 ASP cc_start: 0.7328 (t0) cc_final: 0.6957 (t0) REVERT: A 375 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 479 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7348 (tm-30) REVERT: E 506 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8577 (mm-40) outliers start: 13 outliers final: 9 residues processed: 97 average time/residue: 0.1690 time to fit residues: 23.2990 Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 54 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.182788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150912 restraints weight = 7860.532| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.90 r_work: 0.3503 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6592 Z= 0.177 Angle : 0.490 7.553 8958 Z= 0.238 Chirality : 0.042 0.119 934 Planarity : 0.003 0.042 1165 Dihedral : 3.810 14.907 861 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.87 % Allowed : 15.85 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.57 (0.29), residues: 787 helix: -0.90 (0.28), residues: 361 sheet: -0.94 (0.70), residues: 50 loop : -1.07 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.010 0.001 PHE A 369 TYR 0.013 0.001 TYR E 453 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.669 Fit side-chains REVERT: A 119 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6608 (tp) REVERT: A 157 ASP cc_start: 0.7427 (t0) cc_final: 0.6953 (t0) REVERT: A 332 MET cc_start: 0.8696 (ttp) cc_final: 0.7556 (ttp) REVERT: A 375 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7572 (mm-30) REVERT: A 479 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7577 (tm-30) REVERT: E 506 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8618 (mm-40) outliers start: 13 outliers final: 11 residues processed: 93 average time/residue: 0.1499 time to fit residues: 19.8958 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.183826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150483 restraints weight = 7943.433| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.05 r_work: 0.3458 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6592 Z= 0.239 Angle : 0.525 7.546 8958 Z= 0.255 Chirality : 0.043 0.121 934 Planarity : 0.003 0.046 1165 Dihedral : 4.003 15.688 861 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.45 % Allowed : 16.43 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.53 (0.29), residues: 787 helix: -0.83 (0.28), residues: 364 sheet: -0.52 (0.71), residues: 47 loop : -1.16 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.004 0.001 HIS E 519 PHE 0.011 0.001 PHE A 369 TYR 0.017 0.001 TYR A 202 ARG 0.004 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.687 Fit side-chains REVERT: A 22 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: A 119 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6503 (tp) REVERT: A 323 MET cc_start: 0.7527 (mmm) cc_final: 0.6918 (tpp) REVERT: A 332 MET cc_start: 0.8666 (ttp) cc_final: 0.7529 (ttp) REVERT: A 375 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7463 (mm-30) REVERT: A 479 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7428 (tm-30) REVERT: E 506 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8580 (mm-40) outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 0.1750 time to fit residues: 23.2226 Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 8 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.185713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152655 restraints weight = 7950.577| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.02 r_work: 0.3492 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6592 Z= 0.168 Angle : 0.502 8.321 8958 Z= 0.241 Chirality : 0.042 0.120 934 Planarity : 0.003 0.049 1165 Dihedral : 3.816 14.464 861 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.02 % Allowed : 17.87 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.31 (0.30), residues: 787 helix: -0.62 (0.29), residues: 365 sheet: -0.82 (0.71), residues: 50 loop : -1.01 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.010 0.001 PHE A 369 TYR 0.011 0.001 TYR E 453 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.715 Fit side-chains REVERT: A 22 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 119 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6571 (tp) REVERT: A 323 MET cc_start: 0.7648 (mmm) cc_final: 0.6981 (tpp) REVERT: A 332 MET cc_start: 0.8663 (ttp) cc_final: 0.7490 (ttp) REVERT: A 375 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 479 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7339 (tm-30) REVERT: E 506 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8510 (mm-40) outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 0.1786 time to fit residues: 24.3232 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 0.0000 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 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 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.183670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150673 restraints weight = 7981.044| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.03 r_work: 0.3474 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6592 Z= 0.197 Angle : 0.521 8.182 8958 Z= 0.250 Chirality : 0.042 0.121 934 Planarity : 0.003 0.048 1165 Dihedral : 3.861 14.979 861 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.02 % Allowed : 18.16 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.24 (0.30), residues: 787 helix: -0.52 (0.29), residues: 365 sheet: -0.87 (0.70), residues: 50 loop : -1.00 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 PHE 0.010 0.001 PHE A 369 TYR 0.013 0.001 TYR E 453 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.744 Fit side-chains REVERT: A 22 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: A 119 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6676 (tp) REVERT: A 215 TYR cc_start: 0.7690 (m-80) cc_final: 0.7483 (m-80) REVERT: A 323 MET cc_start: 0.7651 (mmm) cc_final: 0.7035 (tpp) REVERT: A 332 MET cc_start: 0.8653 (ttp) cc_final: 0.7479 (ttp) REVERT: A 375 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7418 (mm-30) REVERT: A 479 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7364 (tm-30) REVERT: E 506 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8527 (mm-40) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 0.1609 time to fit residues: 20.6427 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 57 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.0020 overall best weight: 0.2286 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.188514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155385 restraints weight = 7970.623| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.06 r_work: 0.3527 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6592 Z= 0.119 Angle : 0.479 8.739 8958 Z= 0.230 Chirality : 0.040 0.119 934 Planarity : 0.003 0.048 1165 Dihedral : 3.560 13.029 861 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.02 % Allowed : 18.01 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.99 (0.30), residues: 787 helix: -0.29 (0.29), residues: 366 sheet: -0.74 (0.72), residues: 50 loop : -0.90 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.002 0.000 HIS A 265 PHE 0.010 0.001 PHE A 369 TYR 0.010 0.001 TYR A 215 ARG 0.002 0.000 ARG A 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.780 Fit side-chains REVERT: A 22 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: A 119 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6931 (tp) REVERT: A 323 MET cc_start: 0.7506 (mmm) cc_final: 0.6929 (tpp) REVERT: A 332 MET cc_start: 0.8646 (ttp) cc_final: 0.7833 (ttp) REVERT: A 375 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 479 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7246 (tm-30) REVERT: E 506 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8476 (mm-40) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.1769 time to fit residues: 22.6928 Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 0.0870 chunk 27 optimal weight: 0.0050 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.187034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153731 restraints weight = 8062.400| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.06 r_work: 0.3497 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6592 Z= 0.163 Angle : 0.500 8.748 8958 Z= 0.240 Chirality : 0.041 0.119 934 Planarity : 0.003 0.046 1165 Dihedral : 3.630 13.724 861 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.02 % Allowed : 18.73 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.94 (0.30), residues: 787 helix: -0.24 (0.29), residues: 368 sheet: -0.76 (0.72), residues: 50 loop : -0.88 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.010 0.001 PHE A 369 TYR 0.016 0.001 TYR A 215 ARG 0.003 0.000 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3439.39 seconds wall clock time: 59 minutes 38.88 seconds (3578.88 seconds total)