Starting phenix.real_space_refine on Tue Mar 11 17:10:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrk_34976/03_2025/8hrk_34976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrk_34976/03_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_34976/03_2025/8hrk_34976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrk_34976/03_2025/8hrk_34976.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrk_34976/03_2025/8hrk_34976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrk_34976/03_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-5624/modules/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Time building chain proxies: 5.43, per 1000 atoms: 0.85 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: 1.86 Conformation dependent library (CDL) restraints added in 925.3 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: 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: 0.67 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: 1.87 Time building geometry restraints manager: 2.21 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.380 Find NCS groups from input model: 0.070 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- 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 : 0.795 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: 0.2062 time to fit residues: 25.8630 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 : 0.690 ------------------------------------------------------------------------------- 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 = 0.149887 restraints weight = 7769.233| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.16 r_work: 0.3496 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.578 Fit side-chains REVERT: A 35 GLU cc_start: 0.7883 (tt0) cc_final: 0.7382 (mt-10) REVERT: A 167 SER cc_start: 0.8753 (t) cc_final: 0.7460 (m) REVERT: A 171 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.5759 (mp0) REVERT: A 432 ASN cc_start: 0.7675 (m110) cc_final: 0.6407 (t0) REVERT: E 414 GLN cc_start: 0.7085 (mm-40) cc_final: 0.6197 (mp10) REVERT: E 442 ASP cc_start: 0.8018 (m-30) cc_final: 0.7807 (m-30) outliers start: 28 outliers final: 10 residues processed: 109 average time/residue: 0.1981 time to fit residues: 28.9861 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 : 0.643 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.6980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.189139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.151589 restraints weight = 7829.855| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.47 r_work: 0.3550 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5238 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= 0.196 Angle : 0.549 5.302 8958 Z= 0.297 Chirality : 0.043 0.192 934 Planarity : 0.005 0.067 1165 Dihedral : 5.079 50.566 863 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.45 % Allowed : 20.46 % 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: -2.11 (0.28), residues: 787 helix: -0.66 (0.28), residues: 339 sheet: -1.78 (1.34), residues: 12 loop : -2.06 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 473 HIS 0.006 0.001 HIS A 345 PHE 0.016 0.001 PHE A 327 TYR 0.013 0.001 TYR E 495 ARG 0.002 0.000 ARG A 219 *********************** 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 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 22 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5872 (pt0) REVERT: A 75 GLU cc_start: 0.7129 (tp30) cc_final: 0.6858 (tp30) REVERT: A 123 MET cc_start: 0.8111 (mtt) cc_final: 0.7908 (mtm) REVERT: A 206 ASP cc_start: 0.7354 (t70) cc_final: 0.7144 (t0) outliers start: 17 outliers final: 10 residues processed: 90 average time/residue: 0.1930 time to fit residues: 23.6353 Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 238 GLU 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: 8.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.183791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145944 restraints weight = 7827.317| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.48 r_work: 0.3491 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6592 Z= 0.239 Angle : 0.561 5.722 8958 Z= 0.302 Chirality : 0.043 0.185 934 Planarity : 0.005 0.058 1165 Dihedral : 4.844 49.795 863 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.89 % Allowed : 20.17 % 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: -1.97 (0.28), residues: 787 helix: -0.50 (0.28), residues: 341 sheet: -1.44 (0.93), residues: 22 loop : -2.03 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 473 HIS 0.009 0.001 HIS A 241 PHE 0.015 0.002 PHE A 327 TYR 0.016 0.001 TYR E 495 ARG 0.006 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 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 22 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5839 (pt0) REVERT: A 42 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7259 (mm-40) REVERT: A 75 GLU cc_start: 0.7200 (tp30) cc_final: 0.6925 (tp30) REVERT: A 123 MET cc_start: 0.8044 (mtt) cc_final: 0.7841 (mtm) REVERT: A 206 ASP cc_start: 0.7477 (t70) cc_final: 0.7243 (t0) REVERT: A 345 HIS cc_start: 0.1929 (OUTLIER) cc_final: 0.1408 (t70) REVERT: A 376 MET cc_start: 0.7992 (ttm) cc_final: 0.7742 (mmm) REVERT: A 401 HIS cc_start: 0.9130 (OUTLIER) cc_final: 0.8826 (t70) REVERT: E 472 ILE cc_start: 0.6824 (mm) cc_final: 0.6589 (mm) outliers start: 27 outliers final: 13 residues processed: 102 average time/residue: 0.1899 time to fit residues: 26.3815 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU 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 378 HIS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 485 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.184613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146308 restraints weight = 7860.464| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.59 r_work: 0.3513 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.6275 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= 0.186 Angle : 0.509 5.028 8958 Z= 0.272 Chirality : 0.042 0.153 934 Planarity : 0.005 0.051 1165 Dihedral : 4.611 48.384 863 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.31 % Allowed : 19.60 % 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: -1.67 (0.29), residues: 787 helix: -0.21 (0.29), residues: 340 sheet: -2.51 (0.78), residues: 42 loop : -1.74 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.011 0.001 TYR E 495 ARG 0.009 0.000 ARG A 559 *********************** 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 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.642 Fit side-chains REVERT: A 75 GLU cc_start: 0.7313 (tp30) cc_final: 0.7091 (tp30) REVERT: A 206 ASP cc_start: 0.7544 (t70) cc_final: 0.7267 (t0) REVERT: A 345 HIS cc_start: 0.1663 (OUTLIER) cc_final: 0.1130 (t70) REVERT: A 360 MET cc_start: 0.2607 (tpt) cc_final: 0.0524 (ptt) REVERT: A 531 GLN cc_start: 0.7269 (tp-100) cc_final: 0.6469 (tt0) REVERT: A 548 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.7131 (m) REVERT: E 439 ASN cc_start: 0.8217 (t0) cc_final: 0.7916 (t0) outliers start: 23 outliers final: 15 residues processed: 95 average time/residue: 0.1758 time to fit residues: 23.1085 Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 223 ILE Chi-restraints excluded: chain A residue 334 THR 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 485 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 402 ILE 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: 0.9980 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.0020 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 524 GLN E 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.185979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147887 restraints weight = 7744.537| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.57 r_work: 0.3533 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6592 Z= 0.150 Angle : 0.474 5.409 8958 Z= 0.250 Chirality : 0.040 0.164 934 Planarity : 0.004 0.044 1165 Dihedral : 4.211 46.435 863 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.88 % Allowed : 20.03 % 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: -1.19 (0.30), residues: 787 helix: 0.25 (0.30), residues: 334 sheet: -2.03 (0.84), residues: 40 loop : -1.56 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.004 0.001 HIS A 241 PHE 0.011 0.001 PHE A 327 TYR 0.011 0.001 TYR A 50 ARG 0.005 0.000 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 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.738 Fit side-chains REVERT: A 75 GLU cc_start: 0.7273 (tp30) cc_final: 0.7019 (tp30) REVERT: A 206 ASP cc_start: 0.7532 (t70) cc_final: 0.7258 (t0) REVERT: A 345 HIS cc_start: 0.1432 (OUTLIER) cc_final: 0.0974 (t70) REVERT: A 360 MET cc_start: 0.2659 (tpt) cc_final: 0.0782 (ptm) REVERT: A 531 GLN cc_start: 0.7268 (tp-100) cc_final: 0.6375 (tt0) REVERT: A 534 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7730 (tppt) REVERT: A 548 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6968 (m) REVERT: E 439 ASN cc_start: 0.8317 (t0) cc_final: 0.8024 (t0) outliers start: 20 outliers final: 15 residues processed: 93 average time/residue: 0.1736 time to fit residues: 22.5167 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 485 VAL Chi-restraints excluded: chain A residue 548 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141221 restraints weight = 7695.150| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.58 r_work: 0.3451 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6938 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= 0.226 Angle : 0.551 6.443 8958 Z= 0.294 Chirality : 0.044 0.174 934 Planarity : 0.005 0.046 1165 Dihedral : 4.346 18.468 861 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.31 % Allowed : 19.60 % 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: -1.55 (0.29), residues: 787 helix: -0.08 (0.29), residues: 341 sheet: -2.07 (0.77), residues: 46 loop : -1.76 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 473 HIS 0.009 0.001 HIS A 241 PHE 0.011 0.001 PHE A 28 TYR 0.016 0.001 TYR A 50 ARG 0.005 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 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.736 Fit side-chains REVERT: A 22 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6156 (tt0) REVERT: A 42 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7437 (mm-40) REVERT: A 206 ASP cc_start: 0.7587 (t70) cc_final: 0.7302 (t0) REVERT: A 345 HIS cc_start: 0.1352 (OUTLIER) cc_final: 0.0876 (t70) REVERT: A 360 MET cc_start: 0.3083 (tpt) cc_final: 0.1448 (ptm) REVERT: A 376 MET cc_start: 0.8166 (ttm) cc_final: 0.7837 (mmm) REVERT: A 531 GLN cc_start: 0.7391 (tp-100) cc_final: 0.6466 (tt0) REVERT: A 548 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7358 (m) REVERT: E 408 ARG cc_start: 0.7616 (ptp-170) cc_final: 0.7073 (ptm-80) REVERT: E 439 ASN cc_start: 0.8447 (t0) cc_final: 0.8164 (t0) outliers start: 23 outliers final: 14 residues processed: 90 average time/residue: 0.1789 time to fit residues: 22.5135 Evaluate side-chains 82 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 42 GLN 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 364 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 485 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 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: 2.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.181254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143111 restraints weight = 7757.174| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.59 r_work: 0.3473 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6592 Z= 0.170 Angle : 0.496 5.239 8958 Z= 0.262 Chirality : 0.042 0.167 934 Planarity : 0.004 0.044 1165 Dihedral : 4.019 16.965 861 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.59 % Allowed : 19.74 % 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: -1.21 (0.29), residues: 787 helix: 0.28 (0.30), residues: 334 sheet: -1.65 (0.86), residues: 40 loop : -1.67 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.010 0.001 TYR E 423 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 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.677 Fit side-chains REVERT: A 62 MET cc_start: 0.5242 (mmm) cc_final: 0.4755 (mtm) REVERT: A 206 ASP cc_start: 0.7561 (t70) cc_final: 0.7268 (t0) REVERT: A 345 HIS cc_start: 0.1298 (OUTLIER) cc_final: 0.0875 (t70) REVERT: A 360 MET cc_start: 0.2920 (tpt) cc_final: 0.1638 (ptm) REVERT: A 531 GLN cc_start: 0.7366 (tp-100) cc_final: 0.6510 (tt0) REVERT: A 548 THR cc_start: 0.7371 (OUTLIER) cc_final: 0.7132 (m) REVERT: E 408 ARG cc_start: 0.7573 (ptp-170) cc_final: 0.7039 (ptm-80) REVERT: E 439 ASN cc_start: 0.8478 (t0) cc_final: 0.8226 (t0) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.1607 time to fit residues: 19.8890 Evaluate side-chains 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 366 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 485 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 494 SER 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: 0.4980 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.0000 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.4282 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.183436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144791 restraints weight = 7778.228| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.68 r_work: 0.3493 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.7199 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= 0.145 Angle : 0.475 5.647 8958 Z= 0.249 Chirality : 0.041 0.155 934 Planarity : 0.004 0.041 1165 Dihedral : 3.887 16.445 861 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.88 % Allowed : 19.60 % Favored : 77.52 % 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: -0.95 (0.30), residues: 787 helix: 0.47 (0.30), residues: 336 sheet: -1.48 (1.08), residues: 30 loop : -1.52 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.004 0.001 HIS A 241 PHE 0.011 0.001 PHE A 369 TYR 0.009 0.001 TYR E 423 ARG 0.004 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 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.731 Fit side-chains REVERT: A 42 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7300 (mm-40) REVERT: A 62 MET cc_start: 0.5055 (mmm) cc_final: 0.4429 (mtp) REVERT: A 206 ASP cc_start: 0.7544 (t70) cc_final: 0.7244 (t0) REVERT: A 297 MET cc_start: -0.2772 (ptp) cc_final: -0.3084 (mmm) REVERT: A 345 HIS cc_start: 0.1353 (OUTLIER) cc_final: 0.0862 (t70) REVERT: A 360 MET cc_start: 0.2962 (tpt) cc_final: 0.1758 (ptm) REVERT: A 531 GLN cc_start: 0.7267 (tp-100) cc_final: 0.6350 (tt0) REVERT: A 548 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6930 (m) REVERT: E 408 ARG cc_start: 0.7548 (ptp-170) cc_final: 0.7009 (ptm-80) REVERT: E 439 ASN cc_start: 0.8334 (t0) cc_final: 0.8083 (t0) outliers start: 20 outliers final: 13 residues processed: 88 average time/residue: 0.1745 time to fit residues: 21.3432 Evaluate side-chains 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 176 LEU 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 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 485 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 494 SER 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: 0.8980 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.175725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137486 restraints weight = 7812.785| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.63 r_work: 0.3427 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.7675 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= 0.227 Angle : 0.562 8.518 8958 Z= 0.297 Chirality : 0.044 0.178 934 Planarity : 0.005 0.044 1165 Dihedral : 4.320 15.351 861 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.02 % Allowed : 20.32 % 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: -1.31 (0.29), residues: 787 helix: 0.16 (0.29), residues: 337 sheet: -1.68 (0.79), residues: 46 loop : -1.68 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 473 HIS 0.009 0.001 HIS A 241 PHE 0.019 0.002 PHE A 369 TYR 0.014 0.001 TYR A 385 ARG 0.007 0.001 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 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.664 Fit side-chains REVERT: A 42 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7391 (mm-40) REVERT: A 206 ASP cc_start: 0.7640 (t70) cc_final: 0.7346 (t0) REVERT: A 297 MET cc_start: -0.1887 (ptp) cc_final: -0.4450 (mmm) REVERT: A 345 HIS cc_start: 0.1722 (OUTLIER) cc_final: 0.1200 (t70) REVERT: A 360 MET cc_start: 0.3252 (tpt) cc_final: 0.2363 (ptm) REVERT: A 531 GLN cc_start: 0.7406 (tp-100) cc_final: 0.6507 (tt0) REVERT: E 408 ARG cc_start: 0.7592 (ptp-170) cc_final: 0.7089 (ptm-80) REVERT: E 439 ASN cc_start: 0.8560 (t0) cc_final: 0.8296 (t0) outliers start: 14 outliers final: 12 residues processed: 82 average time/residue: 0.1599 time to fit residues: 18.5199 Evaluate side-chains 81 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 398 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 494 SER 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: 2.9990 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN E 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.178282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140524 restraints weight = 7908.505| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.63 r_work: 0.3446 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.7763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6592 Z= 0.164 Angle : 0.507 7.765 8958 Z= 0.265 Chirality : 0.042 0.162 934 Planarity : 0.004 0.043 1165 Dihedral : 3.978 15.475 861 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.31 % Allowed : 20.32 % Favored : 77.38 % 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: -1.07 (0.30), residues: 787 helix: 0.41 (0.30), residues: 336 sheet: -1.30 (1.08), residues: 30 loop : -1.64 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.014 0.001 PHE A 369 TYR 0.018 0.001 TYR A 50 ARG 0.007 0.000 ARG A 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.96 seconds wall clock time: 55 minutes 41.57 seconds (3341.57 seconds total)