Starting phenix.real_space_refine on Tue Mar 3 18:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wri_32727/03_2026/7wri_32727.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wri_32727/03_2026/7wri_32727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wri_32727/03_2026/7wri_32727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wri_32727/03_2026/7wri_32727.map" model { file = "/net/cci-nas-00/data/ceres_data/7wri_32727/03_2026/7wri_32727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wri_32727/03_2026/7wri_32727.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1565 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4108 2.51 5 N 1080 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6431 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4851 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.33, per 1000 atoms: 0.21 Number of scatterers: 6431 At special positions: 0 Unit cell: (90.2, 81.4, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1205 8.00 N 1080 7.00 C 4108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 229.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 49.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.640A pdb=" N GLU A 35 " --> pdb=" O ASN A 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 removed outlier: 3.893A pdb=" N SER A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.096A pdb=" N ALA A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.585A pdb=" N LYS A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.060A pdb=" N ASP A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 172 removed outlier: 3.676A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.261A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.792A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.876A pdb=" N MET A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.579A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.899A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 383 removed outlier: 4.150A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.512A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.122A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 5.785A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (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 531 removed outlier: 3.532A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.703A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.684A pdb=" N LEU A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.781A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.587A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.623A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.974A 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 347 through 352 removed outlier: 6.276A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.953A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.524A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 1957 1.34 - 1.47: 1856 1.47 - 1.61: 2741 1.61 - 1.74: 0 1.74 - 1.88: 58 Bond restraints: 6612 Sorted by residual: bond pdb=" C ALA A 36 " pdb=" N GLU A 37 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.48e-02 4.57e+03 8.26e+00 bond pdb=" CA ASP A 38 " pdb=" C ASP A 38 " ideal model delta sigma weight residual 1.519 1.486 0.033 1.22e-02 6.72e+03 7.14e+00 bond pdb=" C LEU A 39 " pdb=" O LEU A 39 " ideal model delta sigma weight residual 1.236 1.203 0.034 1.26e-02 6.30e+03 7.11e+00 bond pdb=" C HIS A 353 " pdb=" O HIS A 353 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.44e-02 4.82e+03 5.44e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.44e+00 ... (remaining 6607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 8935 2.95 - 5.91: 42 5.91 - 8.86: 4 8.86 - 11.82: 1 11.82 - 14.77: 1 Bond angle restraints: 8983 Sorted by residual: angle pdb=" C ASP A 38 " pdb=" CA ASP A 38 " pdb=" CB ASP A 38 " ideal model delta sigma weight residual 109.34 97.55 11.79 1.55e+00 4.16e-01 5.79e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 129.17 -14.77 2.30e+00 1.89e-01 4.12e+01 angle pdb=" N ASP A 38 " pdb=" CA ASP A 38 " pdb=" C ASP A 38 " ideal model delta sigma weight residual 113.55 106.33 7.22 1.26e+00 6.30e-01 3.28e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.60 115.51 -6.91 1.46e+00 4.69e-01 2.24e+01 angle pdb=" N LEU A 39 " pdb=" CA LEU A 39 " pdb=" C LEU A 39 " ideal model delta sigma weight residual 111.82 106.92 4.90 1.16e+00 7.43e-01 1.79e+01 ... (remaining 8978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3447 17.86 - 35.71: 372 35.71 - 53.57: 73 53.57 - 71.43: 16 71.43 - 89.28: 11 Dihedral angle restraints: 3919 sinusoidal: 1593 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 36.41 56.59 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" C ASP A 38 " pdb=" N ASP A 38 " pdb=" CA ASP A 38 " pdb=" CB ASP A 38 " ideal model delta harmonic sigma weight residual -122.60 -106.25 -16.35 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" CA LYS A 582 " pdb=" C LYS A 582 " pdb=" N PRO A 583 " pdb=" CA PRO A 583 " ideal model delta harmonic sigma weight residual 180.00 151.27 28.73 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 3916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 807 0.054 - 0.108: 116 0.108 - 0.162: 10 0.162 - 0.217: 1 0.217 - 0.271: 2 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ASP A 38 " pdb=" N ASP A 38 " pdb=" C ASP A 38 " pdb=" CB ASP A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA CYS B 432 " pdb=" N CYS B 432 " pdb=" C CYS B 432 " pdb=" CB CYS B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LEU A 39 " pdb=" N LEU A 39 " pdb=" C LEU A 39 " pdb=" CB LEU A 39 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 933 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 36 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA A 36 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA A 36 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU A 37 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 582 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO A 583 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 146 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.026 5.00e-02 4.00e+02 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 104 2.66 - 3.22: 5639 3.22 - 3.78: 9374 3.78 - 4.34: 13734 4.34 - 4.90: 22185 Nonbonded interactions: 51036 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.099 2.230 nonbonded pdb=" OG1 THR A 365 " pdb=" ND2 ASN A 368 " model vdw 2.258 3.120 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.259 3.040 nonbonded pdb=" O PHE B 490 " pdb=" NH1 ARG B 493 " model vdw 2.270 3.120 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.272 3.040 ... (remaining 51031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.004 0.201 6618 Z= 0.185 Angle : 0.584 14.772 8992 Z= 0.349 Chirality : 0.040 0.271 936 Planarity : 0.004 0.064 1166 Dihedral : 15.538 89.284 2416 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.03 % Allowed : 15.22 % Favored : 82.75 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.24), residues: 786 helix: -2.68 (0.22), residues: 350 sheet: -0.52 (0.72), residues: 43 loop : -3.18 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.012 0.001 TYR A 385 PHE 0.005 0.001 PHE A 588 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6612) covalent geometry : angle 0.57987 ( 8983) SS BOND : bond 0.01110 ( 3) SS BOND : angle 2.77893 ( 6) hydrogen bonds : bond 0.26417 ( 239) hydrogen bonds : angle 7.35108 ( 672) metal coordination : bond 0.20046 ( 2) link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 1.26863 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.246 Fit side-chains REVERT: A 188 ASN cc_start: 0.7948 (m-40) cc_final: 0.7735 (m110) REVERT: A 255 TYR cc_start: 0.8092 (m-80) cc_final: 0.7860 (m-80) REVERT: A 387 ARG cc_start: 0.7881 (ptm160) cc_final: 0.7670 (ptt90) REVERT: A 408 MET cc_start: 0.8615 (mmt) cc_final: 0.8182 (mmt) REVERT: B 378 LYS cc_start: 0.7771 (tptp) cc_final: 0.7543 (tptp) REVERT: B 410 ILE cc_start: 0.8446 (mm) cc_final: 0.8172 (mm) outliers start: 14 outliers final: 12 residues processed: 127 average time/residue: 0.0934 time to fit residues: 15.5095 Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 89 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.145063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115063 restraints weight = 8246.398| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.95 r_work: 0.3232 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6618 Z= 0.164 Angle : 0.599 12.944 8992 Z= 0.309 Chirality : 0.043 0.200 936 Planarity : 0.005 0.073 1166 Dihedral : 5.558 57.844 903 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.32 % Allowed : 17.54 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.27), residues: 786 helix: -1.28 (0.26), residues: 348 sheet: 0.05 (0.71), residues: 43 loop : -2.74 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.017 0.002 TYR B 365 PHE 0.013 0.002 PHE A 390 TRP 0.009 0.001 TRP A 203 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6612) covalent geometry : angle 0.59345 ( 8983) SS BOND : bond 0.00963 ( 3) SS BOND : angle 2.88298 ( 6) hydrogen bonds : bond 0.05110 ( 239) hydrogen bonds : angle 4.42684 ( 672) metal coordination : bond 0.00361 ( 2) link_NAG-ASN : bond 0.00292 ( 1) link_NAG-ASN : angle 2.24377 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.223 Fit side-chains REVERT: A 188 ASN cc_start: 0.7966 (m-40) cc_final: 0.7617 (m110) REVERT: A 408 MET cc_start: 0.8961 (mmt) cc_final: 0.8367 (mmt) REVERT: A 431 ASP cc_start: 0.6595 (p0) cc_final: 0.6370 (p0) REVERT: A 510 TYR cc_start: 0.8968 (m-10) cc_final: 0.8754 (m-10) REVERT: A 609 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7804 (mm-30) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.0931 time to fit residues: 12.1621 Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115172 restraints weight = 8199.824| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.90 r_work: 0.3204 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6618 Z= 0.153 Angle : 0.566 8.672 8992 Z= 0.292 Chirality : 0.042 0.154 936 Planarity : 0.005 0.083 1166 Dihedral : 5.416 57.096 893 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.04 % Allowed : 17.68 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.28), residues: 786 helix: -0.57 (0.28), residues: 342 sheet: 0.27 (0.72), residues: 43 loop : -2.57 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.014 0.001 TYR B 365 PHE 0.017 0.001 PHE A 588 TRP 0.007 0.001 TRP A 594 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6612) covalent geometry : angle 0.56150 ( 8983) SS BOND : bond 0.00708 ( 3) SS BOND : angle 2.54128 ( 6) hydrogen bonds : bond 0.04735 ( 239) hydrogen bonds : angle 4.14960 ( 672) metal coordination : bond 0.00355 ( 2) link_NAG-ASN : bond 0.00147 ( 1) link_NAG-ASN : angle 2.05185 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.241 Fit side-chains REVERT: A 188 ASN cc_start: 0.8022 (m-40) cc_final: 0.7706 (m110) REVERT: A 408 MET cc_start: 0.8996 (mmt) cc_final: 0.8434 (mmt) REVERT: A 609 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7886 (mm-30) REVERT: B 410 ILE cc_start: 0.8706 (mm) cc_final: 0.8424 (mm) outliers start: 21 outliers final: 15 residues processed: 97 average time/residue: 0.0874 time to fit residues: 11.2870 Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 0.0770 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 70 optimal weight: 0.0000 chunk 50 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.149198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119444 restraints weight = 8311.066| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.96 r_work: 0.3299 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 6618 Z= 0.098 Angle : 0.521 14.777 8992 Z= 0.268 Chirality : 0.040 0.183 936 Planarity : 0.005 0.074 1166 Dihedral : 5.018 53.776 892 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.59 % Allowed : 18.55 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.29), residues: 786 helix: -0.07 (0.29), residues: 340 sheet: 0.19 (0.75), residues: 43 loop : -2.22 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.012 0.001 TYR A 385 PHE 0.010 0.001 PHE A 592 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6612) covalent geometry : angle 0.51395 ( 8983) SS BOND : bond 0.01218 ( 3) SS BOND : angle 3.00404 ( 6) hydrogen bonds : bond 0.03393 ( 239) hydrogen bonds : angle 3.92773 ( 672) metal coordination : bond 0.00069 ( 2) link_NAG-ASN : bond 0.00010 ( 1) link_NAG-ASN : angle 1.94154 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.241 Fit side-chains REVERT: A 89 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: A 188 ASN cc_start: 0.8242 (m-40) cc_final: 0.7942 (m110) REVERT: A 387 ARG cc_start: 0.8698 (ptm160) cc_final: 0.8476 (ptt90) REVERT: A 408 MET cc_start: 0.8926 (mmt) cc_final: 0.8499 (mmt) REVERT: A 600 ARG cc_start: 0.7532 (mtp85) cc_final: 0.7327 (mtm110) REVERT: A 609 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 410 ILE cc_start: 0.8651 (mm) cc_final: 0.8337 (mm) outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.0918 time to fit residues: 10.7779 Evaluate side-chains 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.0570 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 65 optimal weight: 0.8980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117198 restraints weight = 8460.775| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.97 r_work: 0.3271 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6618 Z= 0.114 Angle : 0.535 14.650 8992 Z= 0.276 Chirality : 0.041 0.180 936 Planarity : 0.005 0.078 1166 Dihedral : 5.102 55.441 892 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.45 % Allowed : 19.28 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.30), residues: 786 helix: 0.03 (0.29), residues: 348 sheet: 0.23 (0.75), residues: 43 loop : -2.14 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.012 0.001 TYR A 385 PHE 0.011 0.001 PHE A 588 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6612) covalent geometry : angle 0.52921 ( 8983) SS BOND : bond 0.01221 ( 3) SS BOND : angle 2.82517 ( 6) hydrogen bonds : bond 0.03752 ( 239) hydrogen bonds : angle 3.86503 ( 672) metal coordination : bond 0.00225 ( 2) link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 1.81279 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.249 Fit side-chains REVERT: A 89 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: A 188 ASN cc_start: 0.8251 (m-40) cc_final: 0.7926 (m110) REVERT: A 387 ARG cc_start: 0.8757 (ptm160) cc_final: 0.8543 (ptt90) REVERT: A 408 MET cc_start: 0.8954 (mmt) cc_final: 0.8519 (mmt) REVERT: A 609 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8010 (mm-30) REVERT: B 410 ILE cc_start: 0.8634 (mm) cc_final: 0.8352 (mm) outliers start: 10 outliers final: 9 residues processed: 92 average time/residue: 0.0871 time to fit residues: 10.7339 Evaluate side-chains 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.0170 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.117519 restraints weight = 8365.904| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.96 r_work: 0.3260 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 6618 Z= 0.135 Angle : 0.551 14.685 8992 Z= 0.284 Chirality : 0.042 0.180 936 Planarity : 0.005 0.080 1166 Dihedral : 5.257 55.765 892 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.46 % Allowed : 18.84 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.30), residues: 786 helix: 0.10 (0.29), residues: 350 sheet: 0.19 (0.74), residues: 43 loop : -2.10 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.012 0.001 TYR A 385 PHE 0.014 0.001 PHE A 588 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6612) covalent geometry : angle 0.54561 ( 8983) SS BOND : bond 0.01257 ( 3) SS BOND : angle 2.85753 ( 6) hydrogen bonds : bond 0.04109 ( 239) hydrogen bonds : angle 3.91020 ( 672) metal coordination : bond 0.00287 ( 2) link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 1.76278 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.241 Fit side-chains REVERT: A 188 ASN cc_start: 0.8174 (m-40) cc_final: 0.7826 (m110) REVERT: A 408 MET cc_start: 0.8945 (mmt) cc_final: 0.8341 (mmt) REVERT: A 609 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8068 (mm-30) REVERT: B 410 ILE cc_start: 0.8638 (mm) cc_final: 0.8334 (mm) outliers start: 17 outliers final: 16 residues processed: 99 average time/residue: 0.0802 time to fit residues: 10.7353 Evaluate side-chains 100 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115936 restraints weight = 8362.730| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.98 r_work: 0.3227 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6618 Z= 0.149 Angle : 0.572 14.914 8992 Z= 0.295 Chirality : 0.043 0.183 936 Planarity : 0.005 0.083 1166 Dihedral : 5.363 56.048 892 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.32 % Allowed : 19.28 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.30), residues: 786 helix: 0.08 (0.29), residues: 355 sheet: 0.20 (0.75), residues: 43 loop : -2.09 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.012 0.001 TYR A 385 PHE 0.014 0.001 PHE A 588 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6612) covalent geometry : angle 0.56644 ( 8983) SS BOND : bond 0.01290 ( 3) SS BOND : angle 2.91361 ( 6) hydrogen bonds : bond 0.04287 ( 239) hydrogen bonds : angle 3.93791 ( 672) metal coordination : bond 0.00342 ( 2) link_NAG-ASN : bond 0.00123 ( 1) link_NAG-ASN : angle 1.79006 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.200 Fit side-chains REVERT: A 188 ASN cc_start: 0.8089 (m-40) cc_final: 0.7751 (m110) REVERT: A 408 MET cc_start: 0.8944 (mmt) cc_final: 0.8325 (mmt) REVERT: A 549 GLU cc_start: 0.7932 (tp30) cc_final: 0.7651 (mp0) REVERT: A 609 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8097 (mm-30) REVERT: B 410 ILE cc_start: 0.8665 (mm) cc_final: 0.8357 (mm) outliers start: 16 outliers final: 14 residues processed: 99 average time/residue: 0.0847 time to fit residues: 11.1489 Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 24 optimal weight: 8.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118119 restraints weight = 8314.274| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.05 r_work: 0.3245 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 6618 Z= 0.115 Angle : 0.538 14.599 8992 Z= 0.279 Chirality : 0.041 0.177 936 Planarity : 0.005 0.081 1166 Dihedral : 5.200 54.653 892 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.17 % Allowed : 19.86 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.30), residues: 786 helix: 0.21 (0.29), residues: 357 sheet: 0.17 (0.75), residues: 43 loop : -1.95 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.013 0.001 TYR A 385 PHE 0.009 0.001 PHE A 315 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6612) covalent geometry : angle 0.53222 ( 8983) SS BOND : bond 0.01215 ( 3) SS BOND : angle 2.76194 ( 6) hydrogen bonds : bond 0.03720 ( 239) hydrogen bonds : angle 3.85267 ( 672) metal coordination : bond 0.00204 ( 2) link_NAG-ASN : bond 0.00004 ( 1) link_NAG-ASN : angle 1.74953 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.207 Fit side-chains REVERT: A 188 ASN cc_start: 0.8150 (m-40) cc_final: 0.7807 (m110) REVERT: A 408 MET cc_start: 0.8936 (mmt) cc_final: 0.8376 (mmt) REVERT: A 430 GLU cc_start: 0.6164 (mt-10) cc_final: 0.5955 (mt-10) REVERT: A 549 GLU cc_start: 0.7894 (tp30) cc_final: 0.7562 (mp0) REVERT: B 410 ILE cc_start: 0.8646 (mm) cc_final: 0.8342 (mm) outliers start: 15 outliers final: 13 residues processed: 101 average time/residue: 0.0777 time to fit residues: 10.5316 Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117721 restraints weight = 8509.576| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.11 r_work: 0.3237 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6618 Z= 0.117 Angle : 0.545 14.513 8992 Z= 0.282 Chirality : 0.041 0.178 936 Planarity : 0.005 0.081 1166 Dihedral : 5.174 54.706 892 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.17 % Allowed : 20.00 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.30), residues: 786 helix: 0.37 (0.29), residues: 352 sheet: 0.20 (0.75), residues: 43 loop : -1.87 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.013 0.001 TYR A 385 PHE 0.010 0.001 PHE A 523 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6612) covalent geometry : angle 0.53950 ( 8983) SS BOND : bond 0.01223 ( 3) SS BOND : angle 2.75683 ( 6) hydrogen bonds : bond 0.03690 ( 239) hydrogen bonds : angle 3.82927 ( 672) metal coordination : bond 0.00203 ( 2) link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.72089 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.257 Fit side-chains REVERT: A 188 ASN cc_start: 0.8158 (m-40) cc_final: 0.7817 (m110) REVERT: A 408 MET cc_start: 0.8966 (mmt) cc_final: 0.8405 (mmt) REVERT: A 549 GLU cc_start: 0.7918 (tp30) cc_final: 0.7569 (mp0) REVERT: B 410 ILE cc_start: 0.8647 (mm) cc_final: 0.8342 (mm) outliers start: 15 outliers final: 14 residues processed: 95 average time/residue: 0.0665 time to fit residues: 8.7371 Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116107 restraints weight = 8333.502| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.05 r_work: 0.3226 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6618 Z= 0.153 Angle : 0.582 14.748 8992 Z= 0.302 Chirality : 0.043 0.183 936 Planarity : 0.005 0.083 1166 Dihedral : 5.402 56.477 892 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.46 % Allowed : 19.57 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.30), residues: 786 helix: 0.26 (0.29), residues: 355 sheet: 0.22 (0.74), residues: 43 loop : -1.96 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.013 0.001 TYR A 385 PHE 0.014 0.001 PHE A 588 TRP 0.007 0.001 TRP B 436 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6612) covalent geometry : angle 0.57627 ( 8983) SS BOND : bond 0.01285 ( 3) SS BOND : angle 2.87555 ( 6) hydrogen bonds : bond 0.04313 ( 239) hydrogen bonds : angle 3.93420 ( 672) metal coordination : bond 0.00358 ( 2) link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 1.78766 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.292 Fit side-chains REVERT: A 188 ASN cc_start: 0.8045 (m-40) cc_final: 0.7708 (m110) REVERT: A 408 MET cc_start: 0.8922 (mmt) cc_final: 0.8304 (mmt) REVERT: A 549 GLU cc_start: 0.7892 (tp30) cc_final: 0.7617 (mp0) REVERT: B 410 ILE cc_start: 0.8666 (mm) cc_final: 0.8346 (mm) outliers start: 17 outliers final: 15 residues processed: 99 average time/residue: 0.0735 time to fit residues: 10.0613 Evaluate side-chains 101 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116825 restraints weight = 8413.283| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.93 r_work: 0.3235 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 6618 Z= 0.141 Angle : 0.575 14.654 8992 Z= 0.299 Chirality : 0.043 0.182 936 Planarity : 0.005 0.083 1166 Dihedral : 5.380 55.964 892 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.17 % Allowed : 20.00 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.30), residues: 786 helix: 0.25 (0.29), residues: 358 sheet: 0.26 (0.75), residues: 43 loop : -1.88 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.013 0.001 TYR A 385 PHE 0.013 0.001 PHE A 588 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6612) covalent geometry : angle 0.57009 ( 8983) SS BOND : bond 0.01269 ( 3) SS BOND : angle 2.83863 ( 6) hydrogen bonds : bond 0.04106 ( 239) hydrogen bonds : angle 3.92554 ( 672) metal coordination : bond 0.00306 ( 2) link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 1.79487 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2022.14 seconds wall clock time: 35 minutes 13.62 seconds (2113.62 seconds total)