Starting phenix.real_space_refine on Tue Feb 11 17:40:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9i_32367/02_2025/7w9i_32367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9i_32367/02_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_32367/02_2025/7w9i_32367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9i_32367/02_2025/7w9i_32367.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9i_32367/02_2025/7w9i_32367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9i_32367/02_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-5592/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: 4.63, per 1000 atoms: 0.72 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: 1.35 Conformation dependent library (CDL) restraints added in 833.3 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: 0.67 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: 1.72 Time building geometry restraints manager: 1.62 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: 2.120 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.290 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- 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 : 0.699 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: 0.2141 time to fit residues: 34.5633 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 : 0.704 ------------------------------------------------------------------------------- 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 = 0.152927 restraints weight = 7915.386| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.11 r_work: 0.3504 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.654 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8088 (tmm) cc_final: 0.7882 (tmm) REVERT: A 255 TYR cc_start: 0.7578 (m-80) cc_final: 0.7301 (m-10) REVERT: A 332 MET cc_start: 0.8552 (ttp) cc_final: 0.7442 (ttp) REVERT: A 375 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 398 GLU cc_start: 0.8434 (pt0) cc_final: 0.8173 (pt0) REVERT: A 479 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 452 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8144 (mtm180) REVERT: E 508 TYR cc_start: 0.8483 (m-80) cc_final: 0.7827 (m-80) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.1624 time to fit residues: 24.4238 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 : 0.721 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.184129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151931 restraints weight = 8001.419| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.08 r_work: 0.3461 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1976 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= 0.189 Angle : 0.502 7.126 8958 Z= 0.250 Chirality : 0.042 0.149 934 Planarity : 0.004 0.036 1165 Dihedral : 4.105 16.291 861 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.59 % Allowed : 12.54 % Favored : 85.88 % 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: -2.87 (0.27), residues: 787 helix: -2.15 (0.24), residues: 352 sheet: -1.42 (0.67), residues: 47 loop : -1.62 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 PHE 0.012 0.001 PHE E 377 TYR 0.017 0.001 TYR A 202 ARG 0.005 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 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.585 Fit side-chains REVERT: A 157 ASP cc_start: 0.7347 (t0) cc_final: 0.7076 (t0) REVERT: A 255 TYR cc_start: 0.7611 (m-80) cc_final: 0.7379 (m-10) REVERT: A 332 MET cc_start: 0.8654 (ttp) cc_final: 0.7833 (ttp) REVERT: A 375 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 398 GLU cc_start: 0.8487 (pt0) cc_final: 0.8192 (pt0) REVERT: A 479 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7513 (tm-30) REVERT: E 508 TYR cc_start: 0.8474 (m-80) cc_final: 0.7835 (m-80) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.1489 time to fit residues: 20.6210 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 24 optimal weight: 8.9990 chunk 63 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.184888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152082 restraints weight = 8021.116| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.12 r_work: 0.3449 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2197 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= 0.188 Angle : 0.502 7.309 8958 Z= 0.244 Chirality : 0.042 0.123 934 Planarity : 0.003 0.035 1165 Dihedral : 3.988 15.440 861 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.59 % Allowed : 14.70 % Favored : 83.72 % 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: -2.32 (0.28), residues: 787 helix: -1.58 (0.26), residues: 356 sheet: -1.39 (0.68), residues: 50 loop : -1.40 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 PHE 0.009 0.001 PHE A 369 TYR 0.016 0.001 TYR A 202 ARG 0.003 0.000 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 : 0.715 Fit side-chains REVERT: A 157 ASP cc_start: 0.7323 (t0) cc_final: 0.7023 (t0) REVERT: A 255 TYR cc_start: 0.7616 (m-80) cc_final: 0.7371 (m-10) REVERT: A 332 MET cc_start: 0.8639 (ttp) cc_final: 0.7435 (ttp) REVERT: A 375 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 398 GLU cc_start: 0.8546 (pt0) cc_final: 0.8253 (pt0) REVERT: A 479 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7464 (tm-30) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.1626 time to fit residues: 21.4477 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 : 0.699 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.185630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153406 restraints weight = 7953.311| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.07 r_work: 0.3481 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2436 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= 0.146 Angle : 0.480 7.741 8958 Z= 0.233 Chirality : 0.041 0.120 934 Planarity : 0.003 0.037 1165 Dihedral : 3.784 14.178 861 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.16 % Allowed : 14.84 % Favored : 83.00 % 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: -1.87 (0.29), residues: 787 helix: -1.14 (0.27), residues: 357 sheet: -1.13 (0.68), residues: 50 loop : -1.24 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.002 0.001 HIS A 505 PHE 0.009 0.001 PHE A 369 TYR 0.015 0.001 TYR A 202 ARG 0.005 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 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.735 Fit side-chains REVERT: A 119 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6611 (tp) REVERT: A 157 ASP cc_start: 0.7326 (t0) cc_final: 0.7052 (t0) REVERT: A 332 MET cc_start: 0.8627 (ttp) cc_final: 0.7453 (ttp) REVERT: A 375 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 479 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7399 (tm-30) REVERT: E 506 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8591 (mm-40) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.1571 time to fit residues: 21.6079 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain A residue 283 VAL 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 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: 0.5980 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.180413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148629 restraints weight = 7864.375| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.03 r_work: 0.3438 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6592 Z= 0.245 Angle : 0.528 7.262 8958 Z= 0.257 Chirality : 0.043 0.123 934 Planarity : 0.003 0.042 1165 Dihedral : 4.016 16.474 861 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.31 % Allowed : 15.27 % Favored : 82.42 % 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: -1.78 (0.29), residues: 787 helix: -1.08 (0.27), residues: 363 sheet: -0.67 (0.70), residues: 47 loop : -1.24 (0.30), residues: 377 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 0.012 0.001 PHE A 369 TYR 0.018 0.001 TYR E 453 ARG 0.004 0.000 ARG A 514 *********************** 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 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.708 Fit side-chains REVERT: A 22 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: A 119 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6577 (tp) REVERT: A 157 ASP cc_start: 0.7429 (t0) cc_final: 0.6969 (t0) REVERT: A 332 MET cc_start: 0.8633 (ttp) cc_final: 0.7458 (ttp) REVERT: A 375 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7428 (mm-30) REVERT: A 479 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7456 (tm-30) REVERT: E 506 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8597 (mm-40) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 0.1571 time to fit residues: 21.3727 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 : 0.735 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 463 VAL 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: 3.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.182852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150216 restraints weight = 7962.125| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.11 r_work: 0.3429 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6592 Z= 0.255 Angle : 0.540 7.618 8958 Z= 0.262 Chirality : 0.044 0.122 934 Planarity : 0.003 0.044 1165 Dihedral : 4.144 15.668 861 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.31 % Allowed : 16.57 % 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: -1.79 (0.29), residues: 787 helix: -1.07 (0.27), residues: 371 sheet: -0.70 (0.70), residues: 47 loop : -1.25 (0.30), residues: 369 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 0.012 0.001 PHE A 369 TYR 0.019 0.002 TYR A 255 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 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.752 Fit side-chains REVERT: A 22 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 119 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6588 (tp) REVERT: A 157 ASP cc_start: 0.7324 (t0) cc_final: 0.6931 (t0) REVERT: A 323 MET cc_start: 0.7622 (mmm) cc_final: 0.6988 (tpp) REVERT: A 332 MET cc_start: 0.8669 (ttp) cc_final: 0.7453 (ttp) REVERT: A 375 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 400 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8560 (t80) REVERT: A 479 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7476 (tm-30) REVERT: E 506 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8430 (mm110) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.1554 time to fit residues: 21.0118 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 400 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.5980 chunk 66 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.184947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152608 restraints weight = 7936.147| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.11 r_work: 0.3471 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2718 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= 0.159 Angle : 0.497 8.477 8958 Z= 0.238 Chirality : 0.041 0.120 934 Planarity : 0.003 0.043 1165 Dihedral : 3.842 14.674 861 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.16 % Allowed : 17.00 % Favored : 80.84 % 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: -1.50 (0.29), residues: 787 helix: -0.78 (0.28), residues: 369 sheet: -0.95 (0.70), residues: 50 loop : -1.11 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.002 0.001 HIS A 265 PHE 0.010 0.001 PHE A 369 TYR 0.010 0.001 TYR E 453 ARG 0.003 0.000 ARG A 514 *********************** 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 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.661 Fit side-chains REVERT: A 119 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6701 (tp) REVERT: A 323 MET cc_start: 0.7667 (mmm) cc_final: 0.6966 (tpp) REVERT: A 332 MET cc_start: 0.8645 (ttp) cc_final: 0.7469 (ttp) REVERT: A 375 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 479 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7331 (tm-30) REVERT: E 506 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8518 (mm-40) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.1510 time to fit residues: 20.8022 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 11 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.185327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152202 restraints weight = 7993.752| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.06 r_work: 0.3480 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2791 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= 0.163 Angle : 0.504 8.320 8958 Z= 0.242 Chirality : 0.042 0.120 934 Planarity : 0.003 0.043 1165 Dihedral : 3.793 14.276 861 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.02 % Allowed : 17.72 % 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 (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: -1.34 (0.29), residues: 787 helix: -0.59 (0.28), residues: 369 sheet: -0.99 (0.69), residues: 50 loop : -1.08 (0.30), residues: 368 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 0.012 0.001 TYR A 158 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 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.769 Fit side-chains REVERT: A 22 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: A 119 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6723 (tp) REVERT: A 323 MET cc_start: 0.7619 (mmm) cc_final: 0.6965 (tpp) REVERT: A 332 MET cc_start: 0.8632 (ttp) cc_final: 0.7494 (ttp) REVERT: A 375 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 479 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7324 (tm-30) REVERT: E 506 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8534 (mm-40) outliers start: 14 outliers final: 11 residues processed: 91 average time/residue: 0.1968 time to fit residues: 25.6603 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 : 0.761 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 57 optimal weight: 0.0040 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.180791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148358 restraints weight = 7890.047| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.97 r_work: 0.3497 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6592 Z= 0.156 Angle : 0.504 8.727 8958 Z= 0.240 Chirality : 0.041 0.119 934 Planarity : 0.003 0.042 1165 Dihedral : 3.736 13.638 861 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.16 % Allowed : 17.72 % 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: -1.20 (0.30), residues: 787 helix: -0.44 (0.29), residues: 371 sheet: -0.97 (0.69), residues: 50 loop : -1.04 (0.30), residues: 366 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 0.012 0.001 PHE A 400 TYR 0.010 0.001 TYR A 385 ARG 0.003 0.000 ARG A 514 ********************** 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 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.712 Fit side-chains REVERT: A 22 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 119 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6762 (tp) REVERT: A 323 MET cc_start: 0.7538 (mmm) cc_final: 0.6929 (tpp) REVERT: A 325 GLN cc_start: 0.8290 (tp40) cc_final: 0.7831 (tm-30) REVERT: A 332 MET cc_start: 0.8603 (ttp) cc_final: 0.7483 (ttp) REVERT: A 375 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 479 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7306 (tm-30) REVERT: E 506 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8532 (mm-40) outliers start: 15 outliers final: 11 residues processed: 92 average time/residue: 0.1504 time to fit residues: 19.7200 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 27 optimal weight: 0.4980 chunk 57 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.187982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.154818 restraints weight = 8080.118| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.06 r_work: 0.3510 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2951 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= 0.135 Angle : 0.487 8.870 8958 Z= 0.232 Chirality : 0.041 0.119 934 Planarity : 0.003 0.042 1165 Dihedral : 3.641 13.065 861 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: -1.04 (0.30), residues: 787 helix: -0.29 (0.29), residues: 366 sheet: -0.87 (0.70), residues: 50 loop : -0.97 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.009 0.001 PHE A 369 TYR 0.012 0.001 TYR A 215 ARG 0.003 0.000 ARG A 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3069.45 seconds wall clock time: 55 minutes 19.79 seconds (3319.79 seconds total)