Starting phenix.real_space_refine on Thu Jul 2 04:54:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v87_31792/07_2026/7v87_31792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v87_31792/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2026/7v87_31792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2026/7v87_31792.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2026/7v87_31792.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2026/7v87_31792.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2026/7v87_31792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2026/7v87_31792.cif" } 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-6108/lib/python3.11/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 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 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 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 chiralities: 4 Time building chain proxies: 1.50, per 1000 atoms: 0.23 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: 0.53 Conformation dependent library (CDL) restraints added in 372.2 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: 0.18 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: 0.90 Time building geometry restraints manager: 0.71 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 - 17.93: 3481 17.93 - 35.85: 366 35.85 - 53.78: 61 53.78 - 71.71: 10 71.71 - 89.64: 6 Dihedral angle restraints: 3924 sinusoidal: 1586 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 3921 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: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.940 Find NCS groups from input model: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 14.561 89.635 2403 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/Z covalent geometry : bond 0.00342 / 0.17 ( 6799) covalent geometry : angle 0.64590 / 0.34 ( 9239) SS BOND : bond 0.00665 / 0.42 ( 7) SS BOND : angle 1.86885 / 1.57 ( 14) hydrogen bonds : bond 0.14612 / 9.60 ( 281) hydrogen bonds : angle 5.39246 / 3.76 ( 786) link_BETA1-4 : bond 0.00583 / 0.36 ( 5) link_BETA1-4 : angle 1.51426 / 1.07 ( 15) link_NAG-ASN : bond 0.00646 / 0.36 ( 7) link_NAG-ASN : angle 3.25487 / 2.83 ( 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 : 0.252 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: 0.0832 time to fit residues: 6.3449 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 : 0.209 ------------------------------------------------------------------------------- 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... ** 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 = 0.3264 r_free = 0.3264 target = 0.063373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054026 restraints weight = 24159.992| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.41 r_work: 0.2912 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6818 Z= 0.144 Angle : 0.592 10.224 9289 Z= 0.302 Chirality : 0.043 0.263 1002 Planarity : 0.004 0.039 1181 Dihedral : 4.570 26.856 866 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.57 % Allowed : 5.57 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.30), residues: 793 helix: 1.11 (0.28), residues: 384 sheet: 0.17 (0.80), residues: 39 loop : -1.39 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 177 TYR 0.017 0.001 TYR F 50 PHE 0.009 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/Z covalent geometry : bond 0.00322 / 0.14 ( 6799) covalent geometry : angle 0.56863 / 0.30 ( 9239) SS BOND : bond 0.00587 / 0.38 ( 7) SS BOND : angle 1.52131 / 1.01 ( 14) hydrogen bonds : bond 0.05045 / 3.28 ( 281) hydrogen bonds : angle 4.46357 / 3.08 ( 786) link_BETA1-4 : bond 0.00734 / 0.44 ( 5) link_BETA1-4 : angle 1.54457 / 1.00 ( 15) link_NAG-ASN : bond 0.00759 / 0.39 ( 7) link_NAG-ASN : angle 3.05446 / 2.75 ( 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 : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8565 (m-30) cc_final: 0.8342 (m-30) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.0752 time to fit residues: 4.7106 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 : 0.169 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3252 r_free = 0.3252 target = 0.062842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053466 restraints weight = 23940.208| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.39 r_work: 0.2901 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0951 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= 0.140 Angle : 0.566 10.253 9289 Z= 0.288 Chirality : 0.042 0.265 1002 Planarity : 0.004 0.041 1181 Dihedral : 4.543 24.910 866 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.29 % Allowed : 8.71 % Favored : 90.00 % 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: -0.12 (0.30), residues: 793 helix: 1.08 (0.28), residues: 383 sheet: 0.26 (0.80), residues: 39 loop : -1.39 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.015 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/Z covalent geometry : bond 0.00319 / 0.14 ( 6799) covalent geometry : angle 0.54350 / 0.28 ( 9239) SS BOND : bond 0.00398 / 0.23 ( 7) SS BOND : angle 1.35710 / 0.92 ( 14) hydrogen bonds : bond 0.04609 / 2.99 ( 281) hydrogen bonds : angle 4.37350 / 3.02 ( 786) link_BETA1-4 : bond 0.00529 / 0.31 ( 5) link_BETA1-4 : angle 1.58245 / 1.03 ( 15) link_NAG-ASN : bond 0.00706 / 0.36 ( 7) link_NAG-ASN : angle 2.97000 / 2.73 ( 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 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7640 (tpp) REVERT: F 479 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8591 (pm20) outliers start: 9 outliers final: 3 residues processed: 46 average time/residue: 0.0611 time to fit residues: 4.0255 Evaluate side-chains 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.063638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.054176 restraints weight = 23987.575| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.44 r_work: 0.2920 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6818 Z= 0.112 Angle : 0.556 10.302 9289 Z= 0.281 Chirality : 0.041 0.260 1002 Planarity : 0.003 0.041 1181 Dihedral : 4.415 24.186 866 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.43 % Allowed : 10.86 % 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: -0.04 (0.30), residues: 793 helix: 1.16 (0.28), residues: 378 sheet: 0.39 (0.81), residues: 39 loop : -1.35 (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 0.012 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6799) covalent geometry : angle 0.53352 / 0.28 ( 9239) SS BOND : bond 0.00530 / 0.35 ( 7) SS BOND : angle 1.42511 / 0.89 ( 14) hydrogen bonds : bond 0.04058 / 2.59 ( 281) hydrogen bonds : angle 4.25661 / 2.95 ( 786) link_BETA1-4 : bond 0.00465 / 0.27 ( 5) link_BETA1-4 : angle 1.46960 / 0.94 ( 15) link_NAG-ASN : bond 0.00696 / 0.36 ( 7) link_NAG-ASN : angle 2.93923 / 2.73 ( 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 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8538 (m-30) cc_final: 0.8272 (m-30) REVERT: F 323 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7641 (tpp) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.0659 time to fit residues: 4.8686 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 : 0.251 ------------------------------------------------------------------------------- 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 480 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051735 restraints weight = 24627.092| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.43 r_work: 0.2851 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6818 Z= 0.225 Angle : 0.633 10.252 9289 Z= 0.322 Chirality : 0.044 0.275 1002 Planarity : 0.004 0.046 1181 Dihedral : 4.730 23.015 866 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.57 % Allowed : 12.57 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.30), residues: 793 helix: 1.04 (0.28), residues: 383 sheet: 0.46 (0.79), residues: 39 loop : -1.51 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 460 TYR 0.013 0.002 TYR A 453 PHE 0.012 0.001 PHE F 369 TRP 0.009 0.001 TRP F 165 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 ( 6799) covalent geometry : angle 0.61144 / 0.32 ( 9239) SS BOND : bond 0.00516 / 0.31 ( 7) SS BOND : angle 1.66793 / 1.14 ( 14) hydrogen bonds : bond 0.05166 / 3.35 ( 281) hydrogen bonds : angle 4.36565 / 3.02 ( 786) link_BETA1-4 : bond 0.00453 / 0.26 ( 5) link_BETA1-4 : angle 1.62631 / 1.13 ( 15) link_NAG-ASN : bond 0.00740 / 0.40 ( 7) link_NAG-ASN : angle 2.98497 / 2.76 ( 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 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8544 (m-30) cc_final: 0.8322 (m-30) REVERT: F 323 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7940 (tpp) REVERT: F 455 MET cc_start: 0.8921 (tmm) cc_final: 0.8663 (tmm) REVERT: F 479 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8313 (pm20) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 0.0698 time to fit residues: 4.5767 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 136 ASP 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: 0.7980 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.0050 chunk 62 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.053582 restraints weight = 24563.980| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.48 r_work: 0.2900 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6818 Z= 0.110 Angle : 0.560 10.357 9289 Z= 0.282 Chirality : 0.041 0.253 1002 Planarity : 0.004 0.042 1181 Dihedral : 4.576 23.410 866 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.86 % Allowed : 13.14 % Favored : 85.00 % 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: -0.01 (0.30), residues: 793 helix: 1.24 (0.28), residues: 376 sheet: 0.50 (0.78), residues: 42 loop : -1.41 (0.30), residues: 375 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 0.013 0.001 PHE F 72 TRP 0.011 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6799) covalent geometry : angle 0.53863 / 0.28 ( 9239) SS BOND : bond 0.00423 / 0.26 ( 7) SS BOND : angle 1.16530 / 0.77 ( 14) hydrogen bonds : bond 0.04087 / 2.59 ( 281) hydrogen bonds : angle 4.22152 / 2.93 ( 786) link_BETA1-4 : bond 0.00460 / 0.27 ( 5) link_BETA1-4 : angle 1.43373 / 0.93 ( 15) link_NAG-ASN : bond 0.00723 / 0.38 ( 7) link_NAG-ASN : angle 2.95641 / 2.74 ( 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 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8584 (m-30) cc_final: 0.8365 (m-30) REVERT: F 323 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7763 (tpp) REVERT: F 365 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8395 (p) REVERT: F 455 MET cc_start: 0.8865 (tmm) cc_final: 0.8548 (tmm) REVERT: F 479 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8249 (pm20) outliers start: 13 outliers final: 6 residues processed: 51 average time/residue: 0.0639 time to fit residues: 4.7571 Evaluate side-chains 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053092 restraints weight = 24155.113| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.42 r_work: 0.2885 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6818 Z= 0.136 Angle : 0.568 10.404 9289 Z= 0.286 Chirality : 0.042 0.264 1002 Planarity : 0.004 0.043 1181 Dihedral : 4.551 23.152 866 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.71 % Allowed : 14.29 % 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: 0.03 (0.30), residues: 793 helix: 1.25 (0.28), residues: 378 sheet: 0.70 (0.79), residues: 42 loop : -1.40 (0.30), residues: 373 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/Z covalent geometry : bond 0.00309 / 0.14 ( 6799) covalent geometry : angle 0.54636 / 0.28 ( 9239) SS BOND : bond 0.00451 / 0.27 ( 7) SS BOND : angle 1.23447 / 0.83 ( 14) hydrogen bonds : bond 0.04298 / 2.74 ( 281) hydrogen bonds : angle 4.17803 / 2.90 ( 786) link_BETA1-4 : bond 0.00471 / 0.27 ( 5) link_BETA1-4 : angle 1.46598 / 0.98 ( 15) link_NAG-ASN : bond 0.00711 / 0.37 ( 7) link_NAG-ASN : angle 2.95348 / 2.75 ( 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 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8588 (m-30) cc_final: 0.8362 (m-30) REVERT: F 323 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7760 (tpp) REVERT: F 365 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8412 (p) REVERT: F 455 MET cc_start: 0.8903 (tmm) cc_final: 0.8592 (tmm) REVERT: F 479 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8268 (pm20) outliers start: 12 outliers final: 7 residues processed: 49 average time/residue: 0.0731 time to fit residues: 5.0516 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 0.0470 chunk 26 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.063636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.054196 restraints weight = 24257.964| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.45 r_work: 0.2916 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1570 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= 0.103 Angle : 0.545 10.438 9289 Z= 0.271 Chirality : 0.041 0.257 1002 Planarity : 0.003 0.041 1181 Dihedral : 4.404 22.929 866 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.86 % Allowed : 14.43 % Favored : 83.71 % 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: 0.11 (0.30), residues: 793 helix: 1.35 (0.28), residues: 376 sheet: 0.81 (0.80), residues: 42 loop : -1.39 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.010 0.001 TYR F 50 PHE 0.013 0.001 PHE F 72 TRP 0.010 0.001 TRP F 168 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 6799) covalent geometry : angle 0.52336 / 0.27 ( 9239) SS BOND : bond 0.00387 / 0.24 ( 7) SS BOND : angle 1.09858 / 0.72 ( 14) hydrogen bonds : bond 0.03696 / 2.34 ( 281) hydrogen bonds : angle 4.10418 / 2.85 ( 786) link_BETA1-4 : bond 0.00475 / 0.28 ( 5) link_BETA1-4 : angle 1.36254 / 0.87 ( 15) link_NAG-ASN : bond 0.00692 / 0.36 ( 7) link_NAG-ASN : angle 2.93932 / 2.74 ( 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 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8650 (m-30) cc_final: 0.8428 (m-30) REVERT: F 323 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7569 (tpp) REVERT: F 365 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8384 (p) REVERT: F 366 MET cc_start: 0.7995 (ttm) cc_final: 0.7742 (ttm) REVERT: F 455 MET cc_start: 0.8878 (tmm) cc_final: 0.8544 (tmm) REVERT: F 479 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8230 (pm20) outliers start: 13 outliers final: 7 residues processed: 51 average time/residue: 0.0705 time to fit residues: 5.2498 Evaluate side-chains 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.052122 restraints weight = 24431.224| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.41 r_work: 0.2859 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6818 Z= 0.189 Angle : 0.613 10.338 9289 Z= 0.307 Chirality : 0.043 0.270 1002 Planarity : 0.004 0.042 1181 Dihedral : 4.657 23.197 866 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.00 % Allowed : 14.29 % Favored : 83.71 % 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: 0.02 (0.30), residues: 793 helix: 1.26 (0.28), residues: 382 sheet: 1.01 (0.82), residues: 39 loop : -1.49 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 273 TYR 0.012 0.001 TYR A 453 PHE 0.011 0.001 PHE F 369 TRP 0.009 0.001 TRP F 165 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 6799) covalent geometry : angle 0.59278 / 0.30 ( 9239) SS BOND : bond 0.00474 / 0.29 ( 7) SS BOND : angle 1.41274 / 0.95 ( 14) hydrogen bonds : bond 0.04877 / 3.16 ( 281) hydrogen bonds : angle 4.22346 / 2.92 ( 786) link_BETA1-4 : bond 0.00412 / 0.24 ( 5) link_BETA1-4 : angle 1.51538 / 1.05 ( 15) link_NAG-ASN : bond 0.00725 / 0.39 ( 7) link_NAG-ASN : angle 2.98051 / 2.76 ( 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 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: F 227 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: F 323 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7837 (tpp) REVERT: F 365 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8396 (p) REVERT: F 366 MET cc_start: 0.7958 (ttm) cc_final: 0.7644 (ttm) REVERT: F 455 MET cc_start: 0.8968 (tmm) cc_final: 0.8674 (tmm) REVERT: F 479 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8274 (pm20) outliers start: 14 outliers final: 8 residues processed: 51 average time/residue: 0.0650 time to fit residues: 4.9137 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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=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: 2.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.051486 restraints weight = 24561.272| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.41 r_work: 0.2840 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6818 Z= 0.208 Angle : 0.639 10.310 9289 Z= 0.321 Chirality : 0.044 0.263 1002 Planarity : 0.004 0.041 1181 Dihedral : 4.889 23.790 866 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.71 % Allowed : 14.86 % 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: -0.06 (0.30), residues: 793 helix: 1.27 (0.28), residues: 377 sheet: 1.00 (0.84), residues: 39 loop : -1.59 (0.29), residues: 377 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 0.012 0.001 PHE F 369 TRP 0.008 0.001 TRP F 477 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 ( 6799) covalent geometry : angle 0.61804 / 0.32 ( 9239) SS BOND : bond 0.00539 / 0.32 ( 7) SS BOND : angle 1.50693 / 0.99 ( 14) hydrogen bonds : bond 0.05155 / 3.33 ( 281) hydrogen bonds : angle 4.30705 / 2.96 ( 786) link_BETA1-4 : bond 0.00416 / 0.24 ( 5) link_BETA1-4 : angle 1.53857 / 1.07 ( 15) link_NAG-ASN : bond 0.00782 / 0.42 ( 7) link_NAG-ASN : angle 3.04558 / 2.80 ( 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 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: F 227 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: F 323 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8147 (tpp) REVERT: F 365 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8443 (p) REVERT: F 366 MET cc_start: 0.7967 (ttm) cc_final: 0.7718 (tpp) REVERT: F 455 MET cc_start: 0.8969 (tmm) cc_final: 0.8672 (tmm) REVERT: F 479 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8265 (pm20) outliers start: 12 outliers final: 8 residues processed: 48 average time/residue: 0.0672 time to fit residues: 4.6853 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053044 restraints weight = 24313.448| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.43 r_work: 0.2884 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6818 Z= 0.123 Angle : 0.586 10.520 9289 Z= 0.291 Chirality : 0.042 0.252 1002 Planarity : 0.003 0.041 1181 Dihedral : 4.654 23.107 866 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: 0.09 (0.30), residues: 793 helix: 1.43 (0.28), residues: 375 sheet: 1.14 (0.84), residues: 39 loop : -1.55 (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 0.010 0.001 TRP F 163 HIS 0.003 0.001 HIS F 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6799) covalent geometry : angle 0.56461 / 0.29 ( 9239) SS BOND : bond 0.00444 / 0.26 ( 7) SS BOND : angle 1.25109 / 0.81 ( 14) hydrogen bonds : bond 0.04243 / 2.73 ( 281) hydrogen bonds : angle 4.20190 / 2.90 ( 786) link_BETA1-4 : bond 0.00432 / 0.25 ( 5) link_BETA1-4 : angle 1.36962 / 0.89 ( 15) link_NAG-ASN : bond 0.00723 / 0.38 ( 7) link_NAG-ASN : angle 3.01882 / 2.79 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1527.74 seconds wall clock time: 27 minutes 0.79 seconds (1620.79 seconds total)