Starting phenix.real_space_refine on Fri Jun 6 13:50:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wri_32727/06_2025/7wri_32727.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wri_32727/06_2025/7wri_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_32727/06_2025/7wri_32727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wri_32727/06_2025/7wri_32727.map" model { file = "/net/cci-nas-00/data/ceres_data/7wri_32727/06_2025/7wri_32727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wri_32727/06_2025/7wri_32727.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.16, per 1000 atoms: 0.80 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: 1.38 Conformation dependent library (CDL) restraints added in 855.5 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: 0.65 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: 1.70 Time building geometry restraints manager: 1.70 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: 47.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.870 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.830 ------------------------------------------------------------------------------- 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 : 6.76 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 (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: -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 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS A 353 PHE 0.005 0.001 PHE A 588 TYR 0.012 0.001 TYR A 385 ARG 0.001 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 1.26863 ( 3) hydrogen bonds : bond 0.26417 ( 239) hydrogen bonds : angle 7.35108 ( 672) metal coordination : bond 0.20046 ( 2) SS BOND : bond 0.01110 ( 3) SS BOND : angle 2.77893 ( 6) covalent geometry : bond 0.00264 ( 6612) covalent geometry : angle 0.57987 ( 8983) *********************** 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 : 0.810 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: 0.8173 (mm) outliers start: 14 outliers final: 12 residues processed: 127 average time/residue: 0.2341 time to fit residues: 39.0909 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 : 0.811 ------------------------------------------------------------------------------- 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 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.0030 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- 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** A 300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119490 restraints weight = 8197.175| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.93 r_work: 0.3292 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6618 Z= 0.115 Angle : 0.546 12.634 8992 Z= 0.281 Chirality : 0.041 0.198 936 Planarity : 0.005 0.065 1166 Dihedral : 5.228 56.081 903 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.03 % Allowed : 17.54 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.75 (0.27), residues: 786 helix: -1.21 (0.27), residues: 348 sheet: 0.11 (0.75), residues: 43 loop : -2.68 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 203 HIS 0.003 0.001 HIS A 322 PHE 0.013 0.001 PHE A 592 TYR 0.015 0.001 TYR A 510 ARG 0.002 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 1) link_NAG-ASN : angle 2.21510 ( 3) hydrogen bonds : bond 0.04299 ( 239) hydrogen bonds : angle 4.29627 ( 672) metal coordination : bond 0.00492 ( 2) SS BOND : bond 0.00897 ( 3) SS BOND : angle 2.79700 ( 6) covalent geometry : bond 0.00263 ( 6612) covalent geometry : angle 0.54040 ( 8983) *********************** 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 100 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.660 Fit side-chains REVERT: A 188 ASN cc_start: 0.8046 (m-40) cc_final: 0.7706 (m110) REVERT: A 387 ARG cc_start: 0.8674 (ptm160) cc_final: 0.8432 (ptt90) REVERT: A 408 MET cc_start: 0.8936 (mmt) cc_final: 0.8516 (mmt) REVERT: A 510 TYR cc_start: 0.8904 (m-10) cc_final: 0.8699 (m-10) REVERT: A 579 MET cc_start: 0.7737 (mtp) cc_final: 0.7518 (mtm) REVERT: A 609 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7720 (mm-30) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.1955 time to fit residues: 24.7473 Evaluate side-chains 89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 B residue 385 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 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 = 0.145256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116231 restraints weight = 8233.347| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.94 r_work: 0.3225 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6618 Z= 0.144 Angle : 0.572 15.316 8992 Z= 0.294 Chirality : 0.042 0.192 936 Planarity : 0.005 0.078 1166 Dihedral : 5.273 57.468 892 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.32 % Allowed : 17.10 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.17 (0.29), residues: 786 helix: -0.61 (0.28), residues: 349 sheet: 0.18 (0.73), residues: 43 loop : -2.48 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS A 417 PHE 0.012 0.001 PHE A 390 TYR 0.013 0.001 TYR B 365 ARG 0.003 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 1) link_NAG-ASN : angle 1.99842 ( 3) hydrogen bonds : bond 0.04634 ( 239) hydrogen bonds : angle 4.19256 ( 672) metal coordination : bond 0.00295 ( 2) SS BOND : bond 0.01244 ( 3) SS BOND : angle 3.04223 ( 6) covalent geometry : bond 0.00342 ( 6612) covalent geometry : angle 0.56601 ( 8983) *********************** 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 96 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.409 Fit side-chains REVERT: A 188 ASN cc_start: 0.8185 (m-40) cc_final: 0.7875 (m110) REVERT: A 408 MET cc_start: 0.8995 (mmt) cc_final: 0.8420 (mmt) REVERT: A 609 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7758 (mm-30) REVERT: B 410 ILE cc_start: 0.8663 (mm) cc_final: 0.8371 (mm) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.2519 time to fit residues: 31.6007 Evaluate side-chains 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.144150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115777 restraints weight = 8410.999| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.92 r_work: 0.3212 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6618 Z= 0.165 Angle : 0.589 15.014 8992 Z= 0.303 Chirality : 0.043 0.196 936 Planarity : 0.005 0.084 1166 Dihedral : 5.454 57.195 892 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.75 % Allowed : 17.10 % 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 (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: -1.90 (0.29), residues: 786 helix: -0.36 (0.28), residues: 346 sheet: 0.16 (0.76), residues: 41 loop : -2.30 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 610 HIS 0.004 0.001 HIS A 322 PHE 0.015 0.002 PHE A 390 TYR 0.014 0.001 TYR B 365 ARG 0.002 0.000 ARG B 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 1.91551 ( 3) hydrogen bonds : bond 0.04697 ( 239) hydrogen bonds : angle 4.14322 ( 672) metal coordination : bond 0.00390 ( 2) SS BOND : bond 0.01273 ( 3) SS BOND : angle 3.06464 ( 6) covalent geometry : bond 0.00397 ( 6612) covalent geometry : angle 0.58247 ( 8983) *********************** 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 106 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.224 Fit side-chains REVERT: A 188 ASN cc_start: 0.8038 (m-40) cc_final: 0.7758 (m110) REVERT: A 408 MET cc_start: 0.8966 (mmt) cc_final: 0.8353 (mmt) REVERT: A 609 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 357 ARG cc_start: 0.7850 (ttt180) cc_final: 0.7649 (ttp-110) REVERT: B 410 ILE cc_start: 0.8567 (mm) cc_final: 0.8248 (mm) outliers start: 19 outliers final: 16 residues processed: 100 average time/residue: 0.2142 time to fit residues: 30.0737 Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 340 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116181 restraints weight = 8346.812| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.06 r_work: 0.3251 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6618 Z= 0.134 Angle : 0.559 14.162 8992 Z= 0.288 Chirality : 0.042 0.188 936 Planarity : 0.005 0.084 1166 Dihedral : 5.295 55.451 891 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.17 % Allowed : 18.41 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.71 (0.29), residues: 786 helix: -0.28 (0.28), residues: 356 sheet: 0.30 (0.77), residues: 41 loop : -2.17 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A 322 PHE 0.012 0.001 PHE A 390 TYR 0.013 0.001 TYR B 365 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.86886 ( 3) hydrogen bonds : bond 0.04195 ( 239) hydrogen bonds : angle 4.05362 ( 672) metal coordination : bond 0.00294 ( 2) SS BOND : bond 0.01129 ( 3) SS BOND : angle 2.88329 ( 6) covalent geometry : bond 0.00320 ( 6612) covalent geometry : angle 0.55297 ( 8983) *********************** 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 104 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.722 Fit side-chains REVERT: A 188 ASN cc_start: 0.8095 (m-40) cc_final: 0.7762 (m110) REVERT: A 249 MET cc_start: 0.7692 (ttm) cc_final: 0.7388 (ttp) REVERT: A 408 MET cc_start: 0.8942 (mmt) cc_final: 0.8317 (mmt) REVERT: A 609 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8080 (mm-30) REVERT: B 410 ILE cc_start: 0.8665 (mm) cc_final: 0.8377 (mm) outliers start: 15 outliers final: 13 residues processed: 101 average time/residue: 0.1905 time to fit residues: 25.8791 Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 73 optimal weight: 0.0870 chunk 43 optimal weight: 0.4980 chunk 31 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120832 restraints weight = 8290.609| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.02 r_work: 0.3296 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 6618 Z= 0.094 Angle : 0.505 13.036 8992 Z= 0.259 Chirality : 0.040 0.187 936 Planarity : 0.005 0.078 1166 Dihedral : 4.880 53.406 891 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.45 % Allowed : 19.57 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.28 (0.30), residues: 786 helix: 0.13 (0.29), residues: 351 sheet: 0.22 (0.75), residues: 43 loop : -1.94 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.000 HIS A 322 PHE 0.007 0.001 PHE B 374 TYR 0.012 0.001 TYR A 385 ARG 0.003 0.000 ARG A 387 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 1) link_NAG-ASN : angle 1.63396 ( 3) hydrogen bonds : bond 0.03088 ( 239) hydrogen bonds : angle 3.84406 ( 672) metal coordination : bond 0.00062 ( 2) SS BOND : bond 0.01033 ( 3) SS BOND : angle 2.78375 ( 6) covalent geometry : bond 0.00211 ( 6612) covalent geometry : angle 0.49942 ( 8983) *********************** 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 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.101 Fit side-chains REVERT: A 188 ASN cc_start: 0.8127 (m-40) cc_final: 0.7787 (m110) REVERT: A 249 MET cc_start: 0.7592 (ttm) cc_final: 0.7296 (ttp) REVERT: A 408 MET cc_start: 0.8933 (mmt) cc_final: 0.8525 (mmt) REVERT: A 609 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8122 (mm-30) REVERT: B 410 ILE cc_start: 0.8608 (mm) cc_final: 0.8328 (mm) outliers start: 10 outliers final: 8 residues processed: 94 average time/residue: 0.2427 time to fit residues: 31.8901 Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 347 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 59 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118393 restraints weight = 8250.695| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.88 r_work: 0.3256 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6618 Z= 0.117 Angle : 0.532 12.463 8992 Z= 0.274 Chirality : 0.041 0.187 936 Planarity : 0.005 0.082 1166 Dihedral : 4.979 55.060 890 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.03 % Allowed : 19.57 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.30), residues: 786 helix: 0.31 (0.29), residues: 348 sheet: 0.44 (0.76), residues: 43 loop : -1.90 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A 322 PHE 0.020 0.001 PHE A 603 TYR 0.012 0.001 TYR A 385 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 1) link_NAG-ASN : angle 1.75209 ( 3) hydrogen bonds : bond 0.03732 ( 239) hydrogen bonds : angle 3.84779 ( 672) metal coordination : bond 0.00246 ( 2) SS BOND : bond 0.00974 ( 3) SS BOND : angle 2.78651 ( 6) covalent geometry : bond 0.00276 ( 6612) covalent geometry : angle 0.52688 ( 8983) *********************** 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 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.682 Fit side-chains REVERT: A 188 ASN cc_start: 0.8104 (m-40) cc_final: 0.7765 (m110) REVERT: A 249 MET cc_start: 0.7649 (ttm) cc_final: 0.7386 (ttp) REVERT: A 408 MET cc_start: 0.8989 (mmt) cc_final: 0.8569 (mmt) REVERT: A 609 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 410 ILE cc_start: 0.8640 (mm) cc_final: 0.8363 (mm) outliers start: 14 outliers final: 10 residues processed: 93 average time/residue: 0.1670 time to fit residues: 21.3680 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 : 0.662 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain B residue 340 GLU 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 41 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 0.0060 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 40.0000 chunk 4 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118716 restraints weight = 8255.406| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.91 r_work: 0.3257 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6618 Z= 0.115 Angle : 0.538 14.411 8992 Z= 0.277 Chirality : 0.041 0.168 936 Planarity : 0.005 0.081 1166 Dihedral : 4.997 54.753 890 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.03 % Allowed : 19.28 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -0.98 (0.30), residues: 786 helix: 0.39 (0.29), residues: 351 sheet: 0.37 (0.76), residues: 43 loop : -1.79 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A 322 PHE 0.017 0.001 PHE A 603 TYR 0.012 0.001 TYR A 385 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00009 ( 1) link_NAG-ASN : angle 1.71963 ( 3) hydrogen bonds : bond 0.03572 ( 239) hydrogen bonds : angle 3.90576 ( 672) metal coordination : bond 0.00209 ( 2) SS BOND : bond 0.01290 ( 3) SS BOND : angle 3.02190 ( 6) covalent geometry : bond 0.00270 ( 6612) covalent geometry : angle 0.53195 ( 8983) *********************** 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 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.709 Fit side-chains REVERT: A 188 ASN cc_start: 0.8079 (m-40) cc_final: 0.7739 (m110) REVERT: A 408 MET cc_start: 0.8981 (mmt) cc_final: 0.8568 (mmt) REVERT: A 609 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8105 (mm-30) REVERT: B 410 ILE cc_start: 0.8627 (mm) cc_final: 0.8345 (mm) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.1829 time to fit residues: 23.4841 Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 340 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.0770 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 0.0170 chunk 11 optimal weight: 30.0000 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119339 restraints weight = 8423.791| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.94 r_work: 0.3274 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 6618 Z= 0.108 Angle : 0.532 14.272 8992 Z= 0.274 Chirality : 0.041 0.164 936 Planarity : 0.005 0.080 1166 Dihedral : 4.946 54.417 890 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.74 % Allowed : 19.42 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -0.87 (0.31), residues: 786 helix: 0.51 (0.29), residues: 348 sheet: 0.39 (0.77), residues: 43 loop : -1.74 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 322 PHE 0.019 0.001 PHE A 603 TYR 0.012 0.001 TYR A 385 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 1.72189 ( 3) hydrogen bonds : bond 0.03430 ( 239) hydrogen bonds : angle 3.85590 ( 672) metal coordination : bond 0.00164 ( 2) SS BOND : bond 0.01262 ( 3) SS BOND : angle 2.96172 ( 6) covalent geometry : bond 0.00252 ( 6612) covalent geometry : angle 0.52576 ( 8983) *********************** 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 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.683 Fit side-chains REVERT: A 188 ASN cc_start: 0.8058 (m-40) cc_final: 0.7725 (m110) REVERT: A 408 MET cc_start: 0.8972 (mmt) cc_final: 0.8551 (mmt) REVERT: A 609 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8096 (mm-30) REVERT: B 410 ILE cc_start: 0.8622 (mm) cc_final: 0.8333 (mm) outliers start: 12 outliers final: 11 residues processed: 94 average time/residue: 0.1852 time to fit residues: 23.7994 Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 340 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 30.0000 chunk 73 optimal weight: 0.0010 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116393 restraints weight = 8442.415| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.08 r_work: 0.3238 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6618 Z= 0.140 Angle : 0.570 14.649 8992 Z= 0.294 Chirality : 0.042 0.170 936 Planarity : 0.005 0.083 1166 Dihedral : 5.155 56.065 890 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.74 % Allowed : 19.71 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.31), residues: 786 helix: 0.42 (0.29), residues: 350 sheet: 0.41 (0.77), residues: 43 loop : -1.73 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS A 322 PHE 0.019 0.001 PHE A 603 TYR 0.012 0.001 TYR A 385 ARG 0.006 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 1.77036 ( 3) hydrogen bonds : bond 0.04066 ( 239) hydrogen bonds : angle 3.94358 ( 672) metal coordination : bond 0.00309 ( 2) SS BOND : bond 0.01315 ( 3) SS BOND : angle 3.05812 ( 6) covalent geometry : bond 0.00335 ( 6612) covalent geometry : angle 0.56346 ( 8983) ********************** 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 97 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.808 Fit side-chains REVERT: A 188 ASN cc_start: 0.8028 (m-40) cc_final: 0.7687 (m110) REVERT: A 408 MET cc_start: 0.8994 (mmt) cc_final: 0.8421 (mmt) REVERT: A 609 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8139 (mm-30) REVERT: B 410 ILE cc_start: 0.8660 (mm) cc_final: 0.8358 (mm) outliers start: 12 outliers final: 12 residues processed: 94 average time/residue: 0.1721 time to fit residues: 22.5558 Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 340 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119289 restraints weight = 8499.467| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.06 r_work: 0.3272 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6618 Z= 0.108 Angle : 0.540 14.299 8992 Z= 0.278 Chirality : 0.041 0.166 936 Planarity : 0.005 0.081 1166 Dihedral : 4.984 54.386 890 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.74 % Allowed : 19.42 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -0.81 (0.31), residues: 786 helix: 0.55 (0.29), residues: 348 sheet: 0.38 (0.77), residues: 43 loop : -1.69 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 322 PHE 0.018 0.001 PHE A 603 TYR 0.013 0.001 TYR A 385 ARG 0.006 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.67138 ( 3) hydrogen bonds : bond 0.03371 ( 239) hydrogen bonds : angle 3.89508 ( 672) metal coordination : bond 0.00148 ( 2) SS BOND : bond 0.01241 ( 3) SS BOND : angle 2.85997 ( 6) covalent geometry : bond 0.00255 ( 6612) covalent geometry : angle 0.53470 ( 8983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4735.51 seconds wall clock time: 84 minutes 6.51 seconds (5046.51 seconds total)