Starting phenix.real_space_refine on Tue Mar 3 14:59:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9i_32367/03_2026/7w9i_32367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9i_32367/03_2026/7w9i_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_2026/7w9i_32367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9i_32367/03_2026/7w9i_32367.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9i_32367/03_2026/7w9i_32367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9i_32367/03_2026/7w9i_32367.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.47, per 1000 atoms: 0.23 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: 0.56 Conformation dependent library (CDL) restraints added in 196.2 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: 0.21 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: 0.92 Time building geometry restraints manager: 0.73 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: 4.580 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- 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 6599 Z= 0.195 Angle : 0.725 11.787 8972 Z= 0.383 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.007 0.000 ARG A 518 TYR 0.025 0.002 TYR E 453 PHE 0.015 0.002 PHE A 452 TRP 0.010 0.001 TRP A 566 HIS 0.004 0.001 HIS E 519 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6592) covalent geometry : angle 0.72358 ( 8958) SS BOND : bond 0.00315 ( 7) SS BOND : angle 1.33237 ( 14) hydrogen bonds : bond 0.31511 ( 197) hydrogen bonds : angle 11.66894 ( 543) *********************** 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 : 0.238 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: 0.7600 (ptm) REVERT: A 255 TYR cc_start: 0.7287 (m-80) cc_final: 0.7075 (m-10) REVERT: A 375 GLU cc_start: 0.7707 (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: 0.0961 time to fit residues: 15.6213 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 : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 E 493 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151266 restraints weight = 8051.122| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.09 r_work: 0.3458 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6599 Z= 0.140 Angle : 0.529 7.120 8972 Z= 0.268 Chirality : 0.042 0.157 934 Planarity : 0.005 0.044 1165 Dihedral : 4.432 17.557 861 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.30 % Allowed : 11.38 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.24), residues: 787 helix: -3.23 (0.19), residues: 355 sheet: -1.68 (0.73), residues: 45 loop : -1.89 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 514 TYR 0.019 0.001 TYR A 202 PHE 0.015 0.001 PHE E 377 TRP 0.011 0.001 TRP A 566 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6592) covalent geometry : angle 0.52859 ( 8958) SS BOND : bond 0.00331 ( 7) SS BOND : angle 0.81826 ( 14) hydrogen bonds : bond 0.04112 ( 197) hydrogen bonds : angle 5.55333 ( 543) *********************** 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 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 255 TYR cc_start: 0.7597 (m-80) cc_final: 0.7317 (m-10) REVERT: A 332 MET cc_start: 0.8645 (ttp) cc_final: 0.7492 (ttp) REVERT: A 375 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7284 (mm-30) REVERT: A 398 GLU cc_start: 0.8430 (pt0) cc_final: 0.8175 (pt0) REVERT: A 479 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7568 (tm-30) REVERT: E 452 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8260 (mtm180) REVERT: E 508 TYR cc_start: 0.8514 (m-80) cc_final: 0.7865 (m-80) outliers start: 9 outliers final: 5 residues processed: 105 average time/residue: 0.0680 time to fit residues: 10.1810 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 : 0.283 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.3980 chunk 56 optimal weight: 0.1980 chunk 12 optimal weight: 0.0030 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.185743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153744 restraints weight = 7936.281| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.07 r_work: 0.3482 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6599 Z= 0.102 Angle : 0.487 7.279 8972 Z= 0.242 Chirality : 0.041 0.146 934 Planarity : 0.004 0.037 1165 Dihedral : 4.000 15.467 861 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.30 % Allowed : 13.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.27), residues: 787 helix: -2.09 (0.24), residues: 349 sheet: -1.64 (0.67), residues: 50 loop : -1.51 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 514 TYR 0.017 0.001 TYR A 202 PHE 0.011 0.001 PHE E 377 TRP 0.009 0.001 TRP A 566 HIS 0.002 0.000 HIS E 519 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6592) covalent geometry : angle 0.48664 ( 8958) SS BOND : bond 0.00231 ( 7) SS BOND : angle 0.67067 ( 14) hydrogen bonds : bond 0.03466 ( 197) hydrogen bonds : angle 4.79220 ( 543) *********************** 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 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.274 Fit side-chains REVERT: A 157 ASP cc_start: 0.7342 (t0) cc_final: 0.7062 (t0) REVERT: A 255 TYR cc_start: 0.7602 (m-80) cc_final: 0.7382 (m-10) REVERT: A 332 MET cc_start: 0.8650 (ttp) cc_final: 0.7512 (ttp) REVERT: A 375 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7504 (mm-30) REVERT: A 479 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7497 (tm-30) REVERT: E 508 TYR cc_start: 0.8446 (m-80) cc_final: 0.7816 (m-80) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 0.0734 time to fit residues: 10.4535 Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 366 MET 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 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.178537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.146453 restraints weight = 7823.221| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.05 r_work: 0.3440 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6599 Z= 0.159 Angle : 0.521 7.074 8972 Z= 0.256 Chirality : 0.043 0.120 934 Planarity : 0.003 0.035 1165 Dihedral : 4.099 16.845 861 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.31 % Allowed : 14.12 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.28), residues: 787 helix: -1.65 (0.26), residues: 357 sheet: -1.04 (0.70), residues: 47 loop : -1.42 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 514 TYR 0.017 0.001 TYR E 453 PHE 0.013 0.001 PHE A 369 TRP 0.009 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6592) covalent geometry : angle 0.52058 ( 8958) SS BOND : bond 0.00358 ( 7) SS BOND : angle 0.81727 ( 14) hydrogen bonds : bond 0.03518 ( 197) hydrogen bonds : angle 4.63403 ( 543) *********************** 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 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.238 Fit side-chains REVERT: A 157 ASP cc_start: 0.7330 (t0) cc_final: 0.7035 (t0) REVERT: A 255 TYR cc_start: 0.7569 (m-80) cc_final: 0.7358 (m-10) REVERT: A 332 MET cc_start: 0.8663 (ttp) cc_final: 0.7490 (ttp) REVERT: A 375 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 479 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7464 (tm-30) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.0626 time to fit residues: 8.8358 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain A residue 365 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 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 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 70 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.3912 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.183087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151325 restraints weight = 7986.675| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.91 r_work: 0.3510 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6599 Z= 0.102 Angle : 0.487 7.719 8972 Z= 0.237 Chirality : 0.041 0.120 934 Planarity : 0.003 0.038 1165 Dihedral : 3.865 14.590 861 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.45 % Allowed : 14.99 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.28), residues: 787 helix: -1.18 (0.27), residues: 354 sheet: -1.22 (0.68), residues: 50 loop : -1.24 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.015 0.001 TYR A 202 PHE 0.008 0.001 PHE A 369 TRP 0.008 0.001 TRP A 566 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6592) covalent geometry : angle 0.48640 ( 8958) SS BOND : bond 0.00222 ( 7) SS BOND : angle 0.67596 ( 14) hydrogen bonds : bond 0.03131 ( 197) hydrogen bonds : angle 4.37173 ( 543) *********************** 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: 17 poor density : 84 time to evaluate : 0.191 Fit side-chains REVERT: A 157 ASP cc_start: 0.7387 (t0) cc_final: 0.7068 (t0) REVERT: A 323 MET cc_start: 0.7617 (mmm) cc_final: 0.7252 (tpp) REVERT: A 332 MET cc_start: 0.8691 (ttp) cc_final: 0.7523 (ttp) REVERT: A 375 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 479 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7571 (tm-30) REVERT: E 506 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8651 (mm-40) outliers start: 17 outliers final: 13 residues processed: 96 average time/residue: 0.0653 time to fit residues: 9.0646 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 335 LEU 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 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 overall best weight: 0.5500 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.181842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149834 restraints weight = 7999.285| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.97 r_work: 0.3496 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6599 Z= 0.124 Angle : 0.501 7.741 8972 Z= 0.243 Chirality : 0.042 0.120 934 Planarity : 0.003 0.042 1165 Dihedral : 3.883 15.229 861 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.31 % Allowed : 15.71 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.29), residues: 787 helix: -0.98 (0.28), residues: 361 sheet: -1.07 (0.69), residues: 50 loop : -1.14 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.022 0.001 TYR A 202 PHE 0.011 0.001 PHE A 369 TRP 0.008 0.001 TRP A 566 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6592) covalent geometry : angle 0.50010 ( 8958) SS BOND : bond 0.00263 ( 7) SS BOND : angle 0.73560 ( 14) hydrogen bonds : bond 0.03162 ( 197) hydrogen bonds : angle 4.33200 ( 543) *********************** 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 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.229 Fit side-chains REVERT: A 22 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: A 157 ASP cc_start: 0.7446 (t0) cc_final: 0.6987 (t0) REVERT: A 332 MET cc_start: 0.8706 (ttp) cc_final: 0.7523 (ttp) REVERT: A 375 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7604 (mm-30) REVERT: A 479 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7582 (tm-30) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.0631 time to fit residues: 8.7622 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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 335 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.0570 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.182641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151018 restraints weight = 7969.643| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.07 r_work: 0.3476 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6599 Z= 0.114 Angle : 0.493 7.899 8972 Z= 0.239 Chirality : 0.042 0.119 934 Planarity : 0.003 0.046 1165 Dihedral : 3.856 14.297 861 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.02 % Allowed : 16.57 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.29), residues: 787 helix: -0.77 (0.28), residues: 361 sheet: -1.01 (0.69), residues: 50 loop : -1.08 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.019 0.001 TYR A 255 PHE 0.010 0.001 PHE A 400 TRP 0.008 0.001 TRP A 566 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6592) covalent geometry : angle 0.49299 ( 8958) SS BOND : bond 0.00254 ( 7) SS BOND : angle 0.69479 ( 14) hydrogen bonds : bond 0.03041 ( 197) hydrogen bonds : angle 4.23511 ( 543) *********************** 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 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.240 Fit side-chains REVERT: A 22 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: A 157 ASP cc_start: 0.7310 (t0) cc_final: 0.6944 (t0) REVERT: A 323 MET cc_start: 0.7336 (mmm) cc_final: 0.6779 (tpp) REVERT: A 332 MET cc_start: 0.8678 (ttp) cc_final: 0.7845 (ttp) REVERT: A 375 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 479 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7352 (tm-30) outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 0.0653 time to fit residues: 8.6988 Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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 335 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 chunk 4 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.184241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151932 restraints weight = 7989.881| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.11 r_work: 0.3460 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6599 Z= 0.133 Angle : 0.516 8.239 8972 Z= 0.249 Chirality : 0.042 0.121 934 Planarity : 0.003 0.047 1165 Dihedral : 3.899 15.232 861 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.16 % Allowed : 16.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.29), residues: 787 helix: -0.66 (0.29), residues: 361 sheet: -1.00 (0.69), residues: 50 loop : -1.12 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.018 0.001 TYR A 202 PHE 0.010 0.001 PHE A 369 TRP 0.008 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6592) covalent geometry : angle 0.51586 ( 8958) SS BOND : bond 0.00304 ( 7) SS BOND : angle 0.76384 ( 14) hydrogen bonds : bond 0.03144 ( 197) hydrogen bonds : angle 4.27185 ( 543) *********************** 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 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.236 Fit side-chains REVERT: A 22 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: A 157 ASP cc_start: 0.7346 (t0) cc_final: 0.6996 (t0) REVERT: A 332 MET cc_start: 0.8665 (ttp) cc_final: 0.7470 (ttp) REVERT: A 375 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 479 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7349 (tm-30) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.0672 time to fit residues: 8.4188 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 : 0.236 ------------------------------------------------------------------------------- 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 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 335 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 45 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.182425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149404 restraints weight = 8136.647| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.06 r_work: 0.3458 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6599 Z= 0.147 Angle : 0.537 8.336 8972 Z= 0.257 Chirality : 0.043 0.121 934 Planarity : 0.003 0.046 1165 Dihedral : 3.962 15.359 861 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.02 % Allowed : 17.29 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.29), residues: 787 helix: -0.64 (0.29), residues: 364 sheet: -1.05 (0.69), residues: 50 loop : -1.07 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.015 0.001 TYR E 453 PHE 0.011 0.001 PHE A 369 TRP 0.008 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6592) covalent geometry : angle 0.53673 ( 8958) SS BOND : bond 0.00329 ( 7) SS BOND : angle 0.82840 ( 14) hydrogen bonds : bond 0.03199 ( 197) hydrogen bonds : angle 4.36859 ( 543) *********************** 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 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.171 Fit side-chains REVERT: A 22 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: A 157 ASP cc_start: 0.7360 (t0) cc_final: 0.7031 (t0) REVERT: A 332 MET cc_start: 0.8665 (ttp) cc_final: 0.7483 (ttp) REVERT: A 375 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 479 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7358 (tm-30) outliers start: 14 outliers final: 13 residues processed: 84 average time/residue: 0.0602 time to fit residues: 7.2385 Evaluate side-chains 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 335 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.184589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152037 restraints weight = 7887.643| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.13 r_work: 0.3456 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6599 Z= 0.131 Angle : 0.528 8.766 8972 Z= 0.252 Chirality : 0.042 0.121 934 Planarity : 0.003 0.046 1165 Dihedral : 3.890 14.815 861 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.02 % Allowed : 17.29 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.29), residues: 787 helix: -0.60 (0.28), residues: 370 sheet: -1.05 (0.69), residues: 50 loop : -1.10 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.013 0.001 TYR E 453 PHE 0.010 0.001 PHE A 369 TRP 0.009 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6592) covalent geometry : angle 0.52733 ( 8958) SS BOND : bond 0.00291 ( 7) SS BOND : angle 0.77426 ( 14) hydrogen bonds : bond 0.03106 ( 197) hydrogen bonds : angle 4.27939 ( 543) ********************** 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 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.182 Fit side-chains REVERT: A 22 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 157 ASP cc_start: 0.7352 (t0) cc_final: 0.7036 (t0) REVERT: A 332 MET cc_start: 0.8678 (ttp) cc_final: 0.7495 (ttp) REVERT: A 375 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 479 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7353 (tm-30) outliers start: 14 outliers final: 13 residues processed: 88 average time/residue: 0.0610 time to fit residues: 7.6867 Evaluate side-chains 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 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 335 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.0010 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 0.0970 overall best weight: 0.3384 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.186931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154514 restraints weight = 7986.716| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.15 r_work: 0.3485 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6599 Z= 0.095 Angle : 0.499 9.001 8972 Z= 0.238 Chirality : 0.041 0.120 934 Planarity : 0.003 0.046 1165 Dihedral : 3.691 13.410 861 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.87 % Allowed : 17.87 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.30), residues: 787 helix: -0.41 (0.29), residues: 367 sheet: -0.93 (0.70), residues: 50 loop : -1.00 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.015 0.001 TYR A 215 PHE 0.009 0.001 PHE A 369 TRP 0.010 0.001 TRP A 566 HIS 0.002 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6592) covalent geometry : angle 0.49920 ( 8958) SS BOND : bond 0.00212 ( 7) SS BOND : angle 0.64827 ( 14) hydrogen bonds : bond 0.02842 ( 197) hydrogen bonds : angle 4.07964 ( 543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1665.72 seconds wall clock time: 29 minutes 10.96 seconds (1750.96 seconds total)