Starting phenix.real_space_refine on Tue Feb 11 17:38:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrk_34976/02_2025/8hrk_34976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrk_34976/02_2025/8hrk_34976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hrk_34976/02_2025/8hrk_34976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrk_34976/02_2025/8hrk_34976.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrk_34976/02_2025/8hrk_34976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrk_34976/02_2025/8hrk_34976.cif" } resolution = 3.3 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= -0.001 sd= 0.157 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 19 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: (71.38, 88.58, 126.42, 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=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 855.4 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 48.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.720A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 80 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: 3.592A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.823A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.740A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.669A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.577A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.549A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.881A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' 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 299 removed outlier: 3.560A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 4.248A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 4.247A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 330' Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.633A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.543A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.733A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.525A pdb=" N LYS A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.168A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.547A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.747A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.078A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.749A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.767A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.991A 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: 3.977A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.669A 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 406 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.451A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.938A pdb=" N TRP A 349 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.537A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 511 " --> pdb=" O ILE E 434 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 434 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.767A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 597 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: 1.84 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1286 1.33 - 1.45: 1729 1.45 - 1.57: 3516 1.57 - 1.69: 3 1.69 - 1.81: 58 Bond restraints: 6592 Sorted by residual: bond pdb=" CG PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.503 1.208 0.295 3.40e-02 8.65e+02 7.55e+01 bond pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CB PRO A 235 " pdb=" CG PRO A 235 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.59e+00 bond pdb=" CG PRO A 235 " pdb=" CD PRO A 235 " ideal model delta sigma weight residual 1.503 1.416 0.087 3.40e-02 8.65e+02 6.52e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 8926 3.56 - 7.12: 25 7.12 - 10.68: 3 10.68 - 14.24: 2 14.24 - 17.80: 2 Bond angle restraints: 8958 Sorted by residual: angle pdb=" CA PRO A 235 " pdb=" N PRO A 235 " pdb=" CD PRO A 235 " ideal model delta sigma weight residual 112.00 94.20 17.80 1.40e+00 5.10e-01 1.62e+02 angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 85.48 17.72 1.50e+00 4.44e-01 1.40e+02 angle pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 112.00 98.48 13.52 1.40e+00 5.10e-01 9.33e+01 angle pdb=" N PRO A 235 " pdb=" CD PRO A 235 " pdb=" CG PRO A 235 " ideal model delta sigma weight residual 103.20 93.98 9.22 1.50e+00 4.44e-01 3.77e+01 angle pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 104.50 92.97 11.53 1.90e+00 2.77e-01 3.68e+01 ... (remaining 8953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3337 18.00 - 36.00: 432 36.00 - 53.99: 97 53.99 - 71.99: 19 71.99 - 89.99: 8 Dihedral angle restraints: 3893 sinusoidal: 1573 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 176.81 -83.81 1 1.00e+01 1.00e-02 8.57e+01 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 93.00 147.88 -54.88 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -44.04 -41.96 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 414 0.024 - 0.049: 319 0.049 - 0.073: 142 0.073 - 0.097: 35 0.097 - 0.121: 24 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA VAL E 511 " pdb=" N VAL E 511 " pdb=" C VAL E 511 " pdb=" CB VAL E 511 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 931 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.106 5.00e-02 4.00e+02 1.45e-01 3.34e+01 pdb=" N PRO A 235 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " 0.082 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO A 321 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " 0.063 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A 415 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.047 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1697 2.80 - 3.32: 5341 3.32 - 3.85: 9886 3.85 - 4.37: 11141 4.37 - 4.90: 19953 Nonbonded interactions: 48018 Sorted by model distance: nonbonded pdb=" NH1 ARG E 346 " pdb=" O PHE E 347 " model vdw 2.273 3.120 nonbonded pdb=" OE2 GLU A 489 " pdb=" OH TYR A 613 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR E 351 " pdb=" NH2 ARG E 452 " model vdw 2.273 3.120 nonbonded pdb=" OG SER E 371 " pdb=" OG SER E 373 " model vdw 2.288 3.040 nonbonded pdb=" O LEU A 333 " pdb=" OG1 THR A 362 " model vdw 2.293 3.040 ... (remaining 48013 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: 2.500 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.270 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 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 0.295 6592 Z= 0.389 Angle : 0.711 17.801 8958 Z= 0.444 Chirality : 0.040 0.121 934 Planarity : 0.008 0.145 1165 Dihedral : 16.730 89.990 2384 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.14 % Allowed : 17.87 % 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 (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: -1.80 (0.29), residues: 787 helix: -0.48 (0.29), residues: 345 sheet: -2.36 (0.79), residues: 42 loop : -1.69 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 349 HIS 0.001 0.000 HIS A 239 PHE 0.008 0.001 PHE A 369 TYR 0.018 0.001 TYR A 41 ARG 0.002 0.000 ARG A 460 *********************** 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 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.6793 (tt0) cc_final: 0.6416 (mt-10) REVERT: A 376 MET cc_start: 0.7200 (ttt) cc_final: 0.6910 (ttt) REVERT: E 335 LEU cc_start: 0.0534 (OUTLIER) cc_final: -0.0132 (mm) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1914 time to fit residues: 23.6639 Evaluate side-chains 79 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 380 GLN A 432 ASN E 474 GLN E 493 GLN E 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149891 restraints weight = 7769.233| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.16 r_work: 0.3495 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 6592 Z= 0.546 Angle : 0.911 11.283 8958 Z= 0.494 Chirality : 0.055 0.231 934 Planarity : 0.008 0.088 1165 Dihedral : 6.440 49.050 863 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.03 % Allowed : 19.45 % Favored : 76.51 % 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: -2.79 (0.26), residues: 787 helix: -1.41 (0.26), residues: 341 sheet: -1.58 (1.52), residues: 12 loop : -2.28 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 473 HIS 0.020 0.003 HIS A 241 PHE 0.029 0.003 PHE A 230 TYR 0.028 0.003 TYR E 351 ARG 0.007 0.001 ARG A 245 *********************** 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 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.764 Fit side-chains REVERT: A 35 GLU cc_start: 0.7882 (tt0) cc_final: 0.7380 (mt-10) REVERT: A 167 SER cc_start: 0.8755 (t) cc_final: 0.7462 (m) REVERT: A 171 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.5762 (mp0) REVERT: A 432 ASN cc_start: 0.7676 (m110) cc_final: 0.6412 (t0) REVERT: E 414 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6198 (mp10) REVERT: E 442 ASP cc_start: 0.8021 (m-30) cc_final: 0.7809 (m-30) outliers start: 28 outliers final: 10 residues processed: 109 average time/residue: 0.1826 time to fit residues: 26.8417 Evaluate side-chains 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 494 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 380 GLN A 401 HIS E 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.187308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.149506 restraints weight = 7828.888| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.49 r_work: 0.3544 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.210 Angle : 0.559 5.281 8958 Z= 0.303 Chirality : 0.043 0.192 934 Planarity : 0.005 0.071 1165 Dihedral : 5.083 50.582 863 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.16 % Allowed : 20.75 % Favored : 77.09 % 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: -2.15 (0.28), residues: 787 helix: -0.69 (0.28), residues: 339 sheet: -1.89 (1.34), residues: 12 loop : -2.07 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 473 HIS 0.006 0.001 HIS A 241 PHE 0.016 0.002 PHE A 327 TYR 0.014 0.001 TYR E 495 ARG 0.002 0.000 ARG A 273 *********************** 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 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 22 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5857 (pt0) REVERT: A 75 GLU cc_start: 0.7157 (tp30) cc_final: 0.6895 (tp30) REVERT: A 123 MET cc_start: 0.8106 (mtt) cc_final: 0.7886 (mtm) REVERT: A 206 ASP cc_start: 0.7393 (t70) cc_final: 0.7173 (t0) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.1936 time to fit residues: 22.7706 Evaluate side-chains 76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.178954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140880 restraints weight = 7874.817| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.50 r_work: 0.3438 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6592 Z= 0.303 Angle : 0.635 7.108 8958 Z= 0.343 Chirality : 0.046 0.203 934 Planarity : 0.006 0.063 1165 Dihedral : 5.280 49.406 863 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.32 % Allowed : 19.74 % Favored : 75.94 % 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: -2.25 (0.27), residues: 787 helix: -0.80 (0.27), residues: 340 sheet: -1.59 (1.39), residues: 12 loop : -2.12 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 473 HIS 0.011 0.002 HIS A 241 PHE 0.018 0.002 PHE A 230 TYR 0.019 0.002 TYR E 495 ARG 0.007 0.001 ARG A 559 *********************** 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 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.732 Fit side-chains REVERT: A 42 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7349 (mm-40) REVERT: A 75 GLU cc_start: 0.7252 (tp30) cc_final: 0.7015 (tp30) REVERT: A 131 LYS cc_start: 0.5940 (mmtt) cc_final: 0.5709 (mmtt) REVERT: A 163 TRP cc_start: 0.6652 (OUTLIER) cc_final: 0.5184 (p-90) REVERT: A 345 HIS cc_start: 0.1958 (OUTLIER) cc_final: 0.1471 (t70) REVERT: A 360 MET cc_start: 0.2797 (tpt) cc_final: 0.0519 (ptm) REVERT: A 376 MET cc_start: 0.8075 (ttm) cc_final: 0.7837 (mmm) REVERT: A 401 HIS cc_start: 0.9164 (OUTLIER) cc_final: 0.8871 (t70) REVERT: A 531 GLN cc_start: 0.7677 (tp40) cc_final: 0.6914 (tt0) REVERT: E 439 ASN cc_start: 0.8443 (t0) cc_final: 0.8207 (t160) outliers start: 30 outliers final: 16 residues processed: 108 average time/residue: 0.1809 time to fit residues: 26.3193 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.181296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142951 restraints weight = 7816.907| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.61 r_work: 0.3478 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6592 Z= 0.206 Angle : 0.539 5.448 8958 Z= 0.291 Chirality : 0.043 0.186 934 Planarity : 0.005 0.054 1165 Dihedral : 4.888 49.201 863 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.46 % Allowed : 19.60 % Favored : 76.95 % 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: -1.89 (0.29), residues: 787 helix: -0.45 (0.29), residues: 339 sheet: -2.58 (0.73), residues: 46 loop : -1.79 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 473 HIS 0.007 0.001 HIS A 241 PHE 0.014 0.001 PHE E 486 TYR 0.013 0.001 TYR E 495 ARG 0.002 0.000 ARG A 245 *********************** 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 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.726 Fit side-chains REVERT: A 42 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7276 (mm-40) REVERT: A 75 GLU cc_start: 0.7366 (tp30) cc_final: 0.7158 (tp30) REVERT: A 206 ASP cc_start: 0.7587 (t70) cc_final: 0.7329 (t0) REVERT: A 345 HIS cc_start: 0.1645 (OUTLIER) cc_final: 0.1107 (t70) REVERT: A 360 MET cc_start: 0.2771 (tpt) cc_final: 0.0873 (ptm) REVERT: E 439 ASN cc_start: 0.8383 (t0) cc_final: 0.8096 (t0) outliers start: 24 outliers final: 15 residues processed: 100 average time/residue: 0.1850 time to fit residues: 24.9129 Evaluate side-chains 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142110 restraints weight = 7700.192| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.59 r_work: 0.3467 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6592 Z= 0.207 Angle : 0.532 6.223 8958 Z= 0.285 Chirality : 0.043 0.174 934 Planarity : 0.005 0.049 1165 Dihedral : 4.607 46.841 863 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.17 % Allowed : 19.88 % Favored : 76.95 % 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: -1.61 (0.29), residues: 787 helix: -0.16 (0.29), residues: 334 sheet: -2.21 (0.77), residues: 46 loop : -1.72 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 473 HIS 0.008 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.014 0.001 TYR E 495 ARG 0.009 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.713 Fit side-chains REVERT: A 42 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7398 (mm-40) REVERT: A 62 MET cc_start: 0.5036 (mmm) cc_final: 0.4029 (mtm) REVERT: A 206 ASP cc_start: 0.7629 (t70) cc_final: 0.7320 (t0) REVERT: A 345 HIS cc_start: 0.1411 (OUTLIER) cc_final: 0.0947 (t70) REVERT: A 360 MET cc_start: 0.2860 (tpt) cc_final: 0.1572 (ptm) REVERT: A 531 GLN cc_start: 0.7324 (tp-100) cc_final: 0.6454 (tt0) REVERT: A 548 THR cc_start: 0.7422 (OUTLIER) cc_final: 0.7216 (m) REVERT: E 439 ASN cc_start: 0.8468 (t0) cc_final: 0.8211 (t0) outliers start: 22 outliers final: 12 residues processed: 94 average time/residue: 0.1673 time to fit residues: 21.6352 Evaluate side-chains 82 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.175453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136986 restraints weight = 7760.557| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.68 r_work: 0.3402 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.7490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6592 Z= 0.238 Angle : 0.571 6.599 8958 Z= 0.307 Chirality : 0.044 0.174 934 Planarity : 0.005 0.051 1165 Dihedral : 4.836 43.166 863 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.88 % Allowed : 20.17 % Favored : 76.95 % 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: -1.74 (0.29), residues: 787 helix: -0.29 (0.29), residues: 336 sheet: -2.06 (0.78), residues: 46 loop : -1.81 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 473 HIS 0.009 0.001 HIS A 241 PHE 0.015 0.001 PHE A 369 TYR 0.014 0.001 TYR E 495 ARG 0.008 0.001 ARG A 559 *********************** 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 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.676 Fit side-chains REVERT: A 42 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7384 (mm-40) REVERT: A 206 ASP cc_start: 0.7668 (t70) cc_final: 0.7352 (t0) REVERT: A 297 MET cc_start: -0.1947 (ptp) cc_final: -0.3617 (mmm) REVERT: A 345 HIS cc_start: 0.1290 (OUTLIER) cc_final: 0.0870 (t70) REVERT: A 360 MET cc_start: 0.3346 (tpt) cc_final: 0.2416 (ptm) REVERT: A 376 MET cc_start: 0.8143 (ttm) cc_final: 0.7840 (mmm) REVERT: A 531 GLN cc_start: 0.7420 (tp-100) cc_final: 0.6545 (tt0) REVERT: E 439 ASN cc_start: 0.8397 (t0) cc_final: 0.8166 (t0) outliers start: 20 outliers final: 12 residues processed: 97 average time/residue: 0.1742 time to fit residues: 23.0260 Evaluate side-chains 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.0020 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 overall best weight: 0.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN E 394 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.183474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145481 restraints weight = 7752.388| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.67 r_work: 0.3509 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.7448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6592 Z= 0.137 Angle : 0.484 9.047 8958 Z= 0.253 Chirality : 0.041 0.151 934 Planarity : 0.004 0.041 1165 Dihedral : 3.941 16.511 861 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.31 % Allowed : 20.46 % Favored : 77.23 % 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: -1.14 (0.30), residues: 787 helix: 0.37 (0.31), residues: 335 sheet: -1.66 (1.07), residues: 30 loop : -1.67 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.005 0.001 HIS A 378 PHE 0.010 0.001 PHE A 327 TYR 0.016 0.001 TYR A 50 ARG 0.006 0.000 ARG A 559 *********************** 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 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.732 Fit side-chains REVERT: A 141 CYS cc_start: 0.2783 (OUTLIER) cc_final: 0.2447 (t) REVERT: A 206 ASP cc_start: 0.7513 (t70) cc_final: 0.7215 (t0) REVERT: A 345 HIS cc_start: 0.1421 (OUTLIER) cc_final: 0.0963 (t70) REVERT: A 360 MET cc_start: 0.2846 (tpt) cc_final: 0.2041 (ptm) REVERT: A 548 THR cc_start: 0.7119 (OUTLIER) cc_final: 0.6823 (m) outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 0.1625 time to fit residues: 19.7083 Evaluate side-chains 80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.0470 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 43 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN E 448 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.183243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.148431 restraints weight = 7743.445| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.67 r_work: 0.3512 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.7510 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= 0.131 Angle : 0.471 8.539 8958 Z= 0.244 Chirality : 0.040 0.146 934 Planarity : 0.004 0.040 1165 Dihedral : 3.705 15.503 861 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 20.03 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.30), residues: 787 helix: 0.56 (0.31), residues: 336 sheet: -1.41 (1.08), residues: 30 loop : -1.51 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.002 0.000 HIS A 241 PHE 0.018 0.001 PHE A 603 TYR 0.013 0.001 TYR A 50 ARG 0.007 0.000 ARG A 559 *********************** 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 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.652 Fit side-chains REVERT: A 141 CYS cc_start: 0.2944 (OUTLIER) cc_final: 0.2490 (t) REVERT: A 206 ASP cc_start: 0.7472 (t70) cc_final: 0.7173 (t0) REVERT: A 345 HIS cc_start: 0.1516 (OUTLIER) cc_final: 0.1030 (t70) REVERT: A 360 MET cc_start: 0.2979 (tpt) cc_final: 0.2173 (ptm) REVERT: A 470 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7344 (mmtp) REVERT: A 531 GLN cc_start: 0.7193 (tp-100) cc_final: 0.6048 (tt0) REVERT: A 534 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7575 (tppt) REVERT: A 548 THR cc_start: 0.6884 (OUTLIER) cc_final: 0.6539 (m) REVERT: E 439 ASN cc_start: 0.8436 (t0) cc_final: 0.8175 (t0) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.2032 time to fit residues: 23.8931 Evaluate side-chains 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 511 VAL 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: 1.9990 chunk 55 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138287 restraints weight = 7860.058| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.69 r_work: 0.3424 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.7826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6592 Z= 0.194 Angle : 0.529 8.376 8958 Z= 0.278 Chirality : 0.042 0.166 934 Planarity : 0.004 0.044 1165 Dihedral : 4.028 14.865 861 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.87 % Allowed : 20.46 % Favored : 77.67 % 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: -1.06 (0.30), residues: 787 helix: 0.35 (0.30), residues: 337 sheet: -1.56 (0.78), residues: 46 loop : -1.54 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 473 HIS 0.007 0.001 HIS A 241 PHE 0.020 0.001 PHE A 369 TYR 0.014 0.001 TYR A 50 ARG 0.007 0.000 ARG A 559 ********************** 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 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.731 Fit side-chains REVERT: A 141 CYS cc_start: 0.3162 (OUTLIER) cc_final: 0.2762 (t) REVERT: A 206 ASP cc_start: 0.7601 (t70) cc_final: 0.7307 (t0) REVERT: A 345 HIS cc_start: 0.2022 (OUTLIER) cc_final: 0.1345 (t70) REVERT: A 360 MET cc_start: 0.3405 (tpt) cc_final: 0.2734 (ptm) REVERT: A 531 GLN cc_start: 0.7461 (tp-100) cc_final: 0.6387 (tt0) REVERT: A 548 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7271 (m) REVERT: E 439 ASN cc_start: 0.8542 (t0) cc_final: 0.8278 (t0) outliers start: 13 outliers final: 6 residues processed: 82 average time/residue: 0.2424 time to fit residues: 28.2790 Evaluate side-chains 79 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.0040 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.177345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139525 restraints weight = 7941.946| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.68 r_work: 0.3464 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.8025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6592 Z= 0.178 Angle : 0.516 7.818 8958 Z= 0.269 Chirality : 0.042 0.158 934 Planarity : 0.004 0.043 1165 Dihedral : 4.002 14.604 861 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.02 % Allowed : 20.03 % Favored : 77.95 % 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: -1.03 (0.30), residues: 787 helix: 0.36 (0.30), residues: 337 sheet: -1.37 (0.97), residues: 34 loop : -1.54 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.017 0.001 PHE A 369 TYR 0.014 0.001 TYR A 50 ARG 0.002 0.000 ARG A 245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3172.79 seconds wall clock time: 57 minutes 9.49 seconds (3429.49 seconds total)