Starting phenix.real_space_refine on Tue Mar 3 15:51:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v87_31792/03_2026/7v87_31792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v87_31792/03_2026/7v87_31792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v87_31792/03_2026/7v87_31792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v87_31792/03_2026/7v87_31792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v87_31792/03_2026/7v87_31792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v87_31792/03_2026/7v87_31792.map" } resolution = 3.3 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= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4222 2.51 5 N 1085 2.21 5 O 1273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 6617 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.23, per 1000 atoms: 0.19 Number of scatterers: 6617 At special positions: 0 Unit cell: (77, 100.1, 126.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1273 8.00 N 1085 7.00 C 4222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN F 90 " " NAG D 1 " - " ASN F 546 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 103 " " NAG F2003 " - " ASN F 322 " " NAG F2004 " - " ASN F 432 " Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 191.2 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 52.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.513A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.820A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.604A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.740A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 80 removed outlier: 3.644A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 101 removed outlier: 3.811A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 157 through 171 Processing helix chain 'F' and resid 175 through 194 removed outlier: 4.409A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.635A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 231 removed outlier: 3.701A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 251 Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.687A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.878A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.673A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.563A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.750A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 485 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.502A pdb=" N THR F 517 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.680A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.598A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.885A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.024A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'F' and resid 347 through 350 281 hydrogen bonds defined for protein. 786 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: 1.01 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2104 1.35 - 1.47: 1807 1.47 - 1.59: 2830 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6799 Sorted by residual: bond pdb=" C1 NAG F2004 " pdb=" O5 NAG F2004 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C1 NAG F2002 " pdb=" O5 NAG F2002 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 ... (remaining 6794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 9097 2.31 - 4.63: 118 4.63 - 6.94: 22 6.94 - 9.26: 1 9.26 - 11.57: 1 Bond angle restraints: 9239 Sorted by residual: angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 125.97 -11.57 2.30e+00 1.89e-01 2.53e+01 angle pdb=" N GLU F 479 " pdb=" CA GLU F 479 " pdb=" CB GLU F 479 " ideal model delta sigma weight residual 110.28 116.35 -6.07 1.55e+00 4.16e-01 1.54e+01 angle pdb=" C TRP F 478 " pdb=" N GLU F 479 " pdb=" CA GLU F 479 " ideal model delta sigma weight residual 120.31 114.58 5.73 1.52e+00 4.33e-01 1.42e+01 angle pdb=" N ASN F 90 " pdb=" CA ASN F 90 " pdb=" CB ASN F 90 " ideal model delta sigma weight residual 114.17 110.09 4.08 1.14e+00 7.69e-01 1.28e+01 angle pdb=" C THR F 334 " pdb=" N ASP F 335 " pdb=" CA ASP F 335 " ideal model delta sigma weight residual 121.80 129.82 -8.02 2.44e+00 1.68e-01 1.08e+01 ... (remaining 9234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 3812 21.79 - 43.59: 288 43.59 - 65.38: 44 65.38 - 87.17: 18 87.17 - 108.97: 10 Dihedral angle restraints: 4172 sinusoidal: 1834 harmonic: 2338 Sorted by residual: dihedral pdb=" CA PRO F 146 " pdb=" C PRO F 146 " pdb=" N GLY F 147 " pdb=" CA GLY F 147 " ideal model delta harmonic sigma weight residual -180.00 -154.74 -25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA CYS A 379 " pdb=" C CYS A 379 " pdb=" N TYR A 380 " pdb=" CA TYR A 380 " ideal model delta harmonic sigma weight residual 180.00 -156.24 -23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA PHE A 377 " pdb=" C PHE A 377 " pdb=" N LYS A 378 " pdb=" CA LYS A 378 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 4169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 813 0.055 - 0.109: 166 0.109 - 0.164: 15 0.164 - 0.218: 4 0.218 - 0.273: 4 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG F2002 " pdb=" ND2 ASN F 103 " pdb=" C2 NAG F2002 " pdb=" O5 NAG F2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 999 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 521 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 582 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO F 583 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 583 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 583 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 89 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C GLN F 89 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN F 89 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN F 90 " 0.008 2.00e-02 2.50e+03 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 196 2.71 - 3.26: 6592 3.26 - 3.81: 10294 3.81 - 4.35: 12193 4.35 - 4.90: 21047 Nonbonded interactions: 50322 Sorted by model distance: nonbonded pdb=" O LEU F 156 " pdb=" OH TYR F 252 " model vdw 2.167 3.040 nonbonded pdb=" NH1 ARG F 161 " pdb=" O HIS F 265 " model vdw 2.244 3.120 nonbonded pdb=" O SER F 77 " pdb=" NE2 GLN F 81 " model vdw 2.283 3.120 nonbonded pdb=" OG SER F 170 " pdb=" OE1 GLU F 171 " model vdw 2.302 3.040 nonbonded pdb=" NZ LYS A 529 " pdb=" O SER A 530 " model vdw 2.304 3.120 ... (remaining 50317 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } 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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.430 Find NCS groups from input model: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.003 0.036 6818 Z= 0.167 Angle : 0.669 11.570 9289 Z= 0.348 Chirality : 0.046 0.273 1002 Planarity : 0.004 0.036 1181 Dihedral : 16.491 108.968 2651 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.21 (0.30), residues: 793 helix: 1.12 (0.28), residues: 375 sheet: 0.05 (0.79), residues: 42 loop : -1.51 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.015 0.001 TYR A 380 PHE 0.013 0.001 PHE A 347 TRP 0.014 0.001 TRP F 477 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6799) covalent geometry : angle 0.64590 ( 9239) SS BOND : bond 0.00665 ( 7) SS BOND : angle 1.86885 ( 14) hydrogen bonds : bond 0.14612 ( 281) hydrogen bonds : angle 5.39246 ( 786) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 1.51426 ( 15) link_NAG-ASN : bond 0.00646 ( 7) link_NAG-ASN : angle 3.25487 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: F 249 MET cc_start: 0.7919 (tpt) cc_final: 0.7683 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0794 time to fit residues: 6.1174 Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.063318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.053959 restraints weight = 24115.220| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.42 r_work: 0.2912 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6818 Z= 0.143 Angle : 0.609 10.315 9289 Z= 0.305 Chirality : 0.044 0.280 1002 Planarity : 0.004 0.038 1181 Dihedral : 9.985 67.064 1114 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.57 % Allowed : 6.29 % Favored : 93.14 % 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: -0.10 (0.30), residues: 793 helix: 1.08 (0.28), residues: 385 sheet: 0.14 (0.80), residues: 39 loop : -1.36 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 177 TYR 0.017 0.001 TYR F 50 PHE 0.010 0.001 PHE A 347 TRP 0.011 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6799) covalent geometry : angle 0.58311 ( 9239) SS BOND : bond 0.00584 ( 7) SS BOND : angle 1.51047 ( 14) hydrogen bonds : bond 0.04778 ( 281) hydrogen bonds : angle 4.40313 ( 786) link_BETA1-4 : bond 0.00572 ( 5) link_BETA1-4 : angle 2.19359 ( 15) link_NAG-ASN : bond 0.00774 ( 7) link_NAG-ASN : angle 3.05569 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8569 (m-30) cc_final: 0.8327 (m-30) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.0764 time to fit residues: 4.7875 Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.063280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.053922 restraints weight = 23934.428| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.39 r_work: 0.2913 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6818 Z= 0.126 Angle : 0.573 10.314 9289 Z= 0.286 Chirality : 0.043 0.266 1002 Planarity : 0.004 0.041 1181 Dihedral : 7.546 55.805 1114 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.29 % Allowed : 9.29 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.10 (0.30), residues: 793 helix: 1.11 (0.28), residues: 382 sheet: 0.32 (0.81), residues: 39 loop : -1.39 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.014 0.001 TYR F 50 PHE 0.010 0.001 PHE F 72 TRP 0.011 0.001 TRP F 477 HIS 0.004 0.001 HIS F 493 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6799) covalent geometry : angle 0.54831 ( 9239) SS BOND : bond 0.00360 ( 7) SS BOND : angle 1.27042 ( 14) hydrogen bonds : bond 0.04397 ( 281) hydrogen bonds : angle 4.34805 ( 786) link_BETA1-4 : bond 0.00573 ( 5) link_BETA1-4 : angle 2.10890 ( 15) link_NAG-ASN : bond 0.00715 ( 7) link_NAG-ASN : angle 2.96610 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7643 (tpp) outliers start: 9 outliers final: 3 residues processed: 47 average time/residue: 0.0776 time to fit residues: 5.1965 Evaluate side-chains 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 60 optimal weight: 0.0570 chunk 26 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.063912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.054424 restraints weight = 23985.956| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.46 r_work: 0.2926 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6818 Z= 0.108 Angle : 0.563 10.294 9289 Z= 0.281 Chirality : 0.042 0.265 1002 Planarity : 0.003 0.040 1181 Dihedral : 6.420 55.229 1114 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.29 % Allowed : 11.00 % Favored : 87.71 % 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: -0.01 (0.30), residues: 793 helix: 1.18 (0.28), residues: 378 sheet: 0.44 (0.81), residues: 39 loop : -1.33 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.012 0.001 TYR F 50 PHE 0.012 0.001 PHE F 72 TRP 0.011 0.001 TRP F 477 HIS 0.003 0.001 HIS F 493 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6799) covalent geometry : angle 0.53837 ( 9239) SS BOND : bond 0.00522 ( 7) SS BOND : angle 1.39266 ( 14) hydrogen bonds : bond 0.03972 ( 281) hydrogen bonds : angle 4.22509 ( 786) link_BETA1-4 : bond 0.00552 ( 5) link_BETA1-4 : angle 2.00449 ( 15) link_NAG-ASN : bond 0.00722 ( 7) link_NAG-ASN : angle 2.92375 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7604 (tpp) REVERT: F 479 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8289 (pm20) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.0884 time to fit residues: 6.1929 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.063413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.053856 restraints weight = 24505.874| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.50 r_work: 0.2910 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6818 Z= 0.124 Angle : 0.560 10.226 9289 Z= 0.281 Chirality : 0.042 0.270 1002 Planarity : 0.003 0.041 1181 Dihedral : 6.037 55.928 1114 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.29 % Allowed : 12.29 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.30), residues: 793 helix: 1.24 (0.28), residues: 377 sheet: 0.56 (0.81), residues: 39 loop : -1.35 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.012 0.001 TYR F 50 PHE 0.012 0.001 PHE F 72 TRP 0.009 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6799) covalent geometry : angle 0.53740 ( 9239) SS BOND : bond 0.00445 ( 7) SS BOND : angle 1.29541 ( 14) hydrogen bonds : bond 0.04059 ( 281) hydrogen bonds : angle 4.18340 ( 786) link_BETA1-4 : bond 0.00502 ( 5) link_BETA1-4 : angle 1.77285 ( 15) link_NAG-ASN : bond 0.00708 ( 7) link_NAG-ASN : angle 2.90560 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7652 (tpp) REVERT: F 455 MET cc_start: 0.8861 (tmm) cc_final: 0.8582 (tmm) REVERT: F 479 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8278 (pm20) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.0785 time to fit residues: 5.2641 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.063592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054036 restraints weight = 24684.940| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.51 r_work: 0.2909 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6818 Z= 0.121 Angle : 0.546 10.183 9289 Z= 0.275 Chirality : 0.041 0.268 1002 Planarity : 0.003 0.042 1181 Dihedral : 5.971 55.928 1114 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.86 % Allowed : 13.00 % Favored : 85.14 % 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: 0.09 (0.30), residues: 793 helix: 1.31 (0.28), residues: 376 sheet: 0.70 (0.81), residues: 39 loop : -1.36 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.010 0.001 TYR F 50 PHE 0.012 0.001 PHE F 72 TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6799) covalent geometry : angle 0.52409 ( 9239) SS BOND : bond 0.00406 ( 7) SS BOND : angle 1.17215 ( 14) hydrogen bonds : bond 0.04014 ( 281) hydrogen bonds : angle 4.12814 ( 786) link_BETA1-4 : bond 0.00525 ( 5) link_BETA1-4 : angle 1.63303 ( 15) link_NAG-ASN : bond 0.00703 ( 7) link_NAG-ASN : angle 2.89760 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7633 (tpp) REVERT: F 365 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8396 (p) REVERT: F 455 MET cc_start: 0.8862 (tmm) cc_final: 0.8548 (tmm) REVERT: F 479 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8281 (pm20) outliers start: 13 outliers final: 7 residues processed: 52 average time/residue: 0.0773 time to fit residues: 5.7535 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 0.0000 chunk 42 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.063893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054407 restraints weight = 24138.568| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.46 r_work: 0.2920 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6818 Z= 0.111 Angle : 0.549 10.154 9289 Z= 0.275 Chirality : 0.041 0.267 1002 Planarity : 0.003 0.041 1181 Dihedral : 5.885 55.504 1114 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.86 % Allowed : 13.71 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.30), residues: 793 helix: 1.37 (0.28), residues: 375 sheet: 0.82 (0.81), residues: 39 loop : -1.36 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.010 0.001 TYR F 50 PHE 0.012 0.001 PHE F 72 TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 493 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6799) covalent geometry : angle 0.52759 ( 9239) SS BOND : bond 0.00380 ( 7) SS BOND : angle 1.12520 ( 14) hydrogen bonds : bond 0.03822 ( 281) hydrogen bonds : angle 4.09001 ( 786) link_BETA1-4 : bond 0.00512 ( 5) link_BETA1-4 : angle 1.56923 ( 15) link_NAG-ASN : bond 0.00702 ( 7) link_NAG-ASN : angle 2.87893 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7582 (tpp) REVERT: F 365 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8461 (p) REVERT: F 455 MET cc_start: 0.8868 (tmm) cc_final: 0.8553 (tmm) REVERT: F 479 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8279 (pm20) outliers start: 13 outliers final: 8 residues processed: 55 average time/residue: 0.0732 time to fit residues: 5.7122 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 4.9990 chunk 19 optimal weight: 0.0170 chunk 71 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 0.0020 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056924 restraints weight = 24613.273| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.54 r_work: 0.2964 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6818 Z= 0.093 Angle : 0.544 10.152 9289 Z= 0.267 Chirality : 0.041 0.265 1002 Planarity : 0.003 0.036 1181 Dihedral : 5.708 53.748 1114 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.57 % Allowed : 13.43 % Favored : 84.00 % 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: 0.23 (0.30), residues: 793 helix: 1.42 (0.28), residues: 374 sheet: 0.82 (0.81), residues: 42 loop : -1.28 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.011 0.001 TYR F 50 PHE 0.014 0.001 PHE F 72 TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 493 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 6799) covalent geometry : angle 0.52381 ( 9239) SS BOND : bond 0.00327 ( 7) SS BOND : angle 0.96449 ( 14) hydrogen bonds : bond 0.03202 ( 281) hydrogen bonds : angle 4.04459 ( 786) link_BETA1-4 : bond 0.00549 ( 5) link_BETA1-4 : angle 1.41942 ( 15) link_NAG-ASN : bond 0.00672 ( 7) link_NAG-ASN : angle 2.84545 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: F 97 LEU cc_start: 0.9471 (tp) cc_final: 0.9253 (tp) REVERT: F 365 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8382 (p) REVERT: F 455 MET cc_start: 0.8833 (tmm) cc_final: 0.8495 (tmm) REVERT: F 479 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8248 (pm20) outliers start: 18 outliers final: 9 residues processed: 63 average time/residue: 0.0792 time to fit residues: 6.9583 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.0020 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 = 0.3269 r_free = 0.3269 target = 0.064803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055573 restraints weight = 24764.539| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.68 r_work: 0.2913 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6818 Z= 0.143 Angle : 0.583 10.015 9289 Z= 0.288 Chirality : 0.043 0.277 1002 Planarity : 0.003 0.040 1181 Dihedral : 5.872 56.055 1114 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.86 % Allowed : 14.71 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.24 (0.30), residues: 793 helix: 1.47 (0.28), residues: 377 sheet: 1.08 (0.83), residues: 39 loop : -1.37 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.011 0.001 TYR F 50 PHE 0.011 0.001 PHE F 72 TRP 0.010 0.001 TRP F 165 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6799) covalent geometry : angle 0.56276 ( 9239) SS BOND : bond 0.00367 ( 7) SS BOND : angle 1.20003 ( 14) hydrogen bonds : bond 0.04082 ( 281) hydrogen bonds : angle 4.05074 ( 786) link_BETA1-4 : bond 0.00525 ( 5) link_BETA1-4 : angle 1.54214 ( 15) link_NAG-ASN : bond 0.00685 ( 7) link_NAG-ASN : angle 2.85069 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.8174 (tpp) cc_final: 0.7780 (tpp) REVERT: F 365 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8473 (p) REVERT: F 455 MET cc_start: 0.8929 (tmm) cc_final: 0.8621 (tmm) REVERT: F 479 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8281 (pm20) outliers start: 13 outliers final: 9 residues processed: 51 average time/residue: 0.0706 time to fit residues: 5.3697 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.062011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.052572 restraints weight = 24437.091| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.42 r_work: 0.2872 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6818 Z= 0.176 Angle : 0.629 10.003 9289 Z= 0.312 Chirality : 0.044 0.270 1002 Planarity : 0.004 0.041 1181 Dihedral : 6.106 57.552 1114 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.71 % Allowed : 15.00 % Favored : 83.29 % 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: 0.12 (0.30), residues: 793 helix: 1.35 (0.28), residues: 383 sheet: 1.05 (0.82), residues: 39 loop : -1.45 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.012 0.001 TYR A 453 PHE 0.011 0.001 PHE F 369 TRP 0.008 0.001 TRP F 165 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6799) covalent geometry : angle 0.60950 ( 9239) SS BOND : bond 0.00462 ( 7) SS BOND : angle 1.38844 ( 14) hydrogen bonds : bond 0.04764 ( 281) hydrogen bonds : angle 4.18927 ( 786) link_BETA1-4 : bond 0.00493 ( 5) link_BETA1-4 : angle 1.64713 ( 15) link_NAG-ASN : bond 0.00755 ( 7) link_NAG-ASN : angle 2.88496 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.8536 (tpp) cc_final: 0.8250 (tpp) REVERT: F 365 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8497 (p) REVERT: F 455 MET cc_start: 0.8946 (tmm) cc_final: 0.8648 (tmm) REVERT: F 479 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8277 (pm20) outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.0625 time to fit residues: 4.7277 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.063221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.053779 restraints weight = 24235.270| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.45 r_work: 0.2906 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6818 Z= 0.120 Angle : 0.584 10.039 9289 Z= 0.287 Chirality : 0.042 0.263 1002 Planarity : 0.003 0.039 1181 Dihedral : 5.971 56.003 1114 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.57 % Allowed : 15.29 % Favored : 83.14 % 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: 0.23 (0.30), residues: 793 helix: 1.52 (0.28), residues: 375 sheet: 1.17 (0.84), residues: 39 loop : -1.43 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.010 0.001 TYR F 50 PHE 0.012 0.001 PHE F 72 TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 493 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6799) covalent geometry : angle 0.56469 ( 9239) SS BOND : bond 0.00441 ( 7) SS BOND : angle 1.19582 ( 14) hydrogen bonds : bond 0.04006 ( 281) hydrogen bonds : angle 4.11212 ( 786) link_BETA1-4 : bond 0.00513 ( 5) link_BETA1-4 : angle 1.50569 ( 15) link_NAG-ASN : bond 0.00712 ( 7) link_NAG-ASN : angle 2.85357 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1620.32 seconds wall clock time: 28 minutes 23.82 seconds (1703.82 seconds total)