Starting phenix.real_space_refine on Tue Feb 11 22:59:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v87_31792/02_2025/7v87_31792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v87_31792/02_2025/7v87_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_31792/02_2025/7v87_31792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v87_31792/02_2025/7v87_31792.map" model { file = "/net/cci-nas-00/data/ceres_data/7v87_31792/02_2025/7v87_31792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v87_31792/02_2025/7v87_31792.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.29, per 1000 atoms: 0.80 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: 1.76 Conformation dependent library (CDL) restraints added in 886.5 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: 0.83 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: 1.94 Time building geometry restraints manager: 2.03 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- 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 6799 Z= 0.214 Angle : 0.646 11.570 9239 Z= 0.342 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 : 6.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (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 TRP 0.014 0.001 TRP F 477 HIS 0.005 0.001 HIS F 374 PHE 0.013 0.001 PHE A 347 TYR 0.015 0.001 TYR A 380 ARG 0.002 0.000 ARG A 403 *********************** 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 : 0.685 Fit side-chains revert: symmetry clash REVERT: F 249 MET cc_start: 0.7919 (tpt) cc_final: 0.7684 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2041 time to fit residues: 15.4846 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 : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.061193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051884 restraints weight = 24171.835| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.36 r_work: 0.2857 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6799 Z= 0.359 Angle : 0.648 7.826 9239 Z= 0.336 Chirality : 0.047 0.291 1002 Planarity : 0.004 0.042 1181 Dihedral : 10.126 66.594 1114 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.57 % Allowed : 7.29 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.30), residues: 793 helix: 0.98 (0.28), residues: 389 sheet: 0.04 (0.78), residues: 39 loop : -1.55 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 477 HIS 0.004 0.001 HIS F 378 PHE 0.014 0.001 PHE A 347 TYR 0.016 0.002 TYR F 50 ARG 0.003 0.000 ARG F 460 *********************** 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 : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8520 (m-30) cc_final: 0.8173 (m-30) REVERT: F 82 MET cc_start: 0.8646 (mpp) cc_final: 0.8438 (mpp) REVERT: F 479 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8445 (pm20) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 0.1852 time to fit residues: 11.8812 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 : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 212 VAL 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 8 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** F 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.062448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053114 restraints weight = 24005.083| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.41 r_work: 0.2893 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6799 Z= 0.189 Angle : 0.558 7.698 9239 Z= 0.287 Chirality : 0.043 0.258 1002 Planarity : 0.004 0.042 1181 Dihedral : 7.634 56.408 1114 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.29 % Allowed : 10.00 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.30), residues: 793 helix: 1.00 (0.28), residues: 384 sheet: 0.19 (0.79), residues: 39 loop : -1.46 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 PHE 0.011 0.001 PHE F 72 TYR 0.015 0.001 TYR F 50 ARG 0.002 0.000 ARG F 460 *********************** 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 : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 401 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.8454 (t-90) outliers start: 9 outliers final: 3 residues processed: 48 average time/residue: 0.1823 time to fit residues: 12.7134 Evaluate side-chains 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 401 HIS 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 60 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 58 ASN ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.053115 restraints weight = 24348.594| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.44 r_work: 0.2889 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6799 Z= 0.211 Angle : 0.557 8.468 9239 Z= 0.287 Chirality : 0.043 0.263 1002 Planarity : 0.004 0.044 1181 Dihedral : 6.545 56.477 1114 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.29 % Allowed : 12.00 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.30), residues: 793 helix: 0.99 (0.28), residues: 384 sheet: 0.23 (0.78), residues: 39 loop : -1.46 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.011 0.001 PHE F 72 TYR 0.013 0.001 TYR F 50 ARG 0.002 0.000 ARG F 460 *********************** 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 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: F 401 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8450 (t-90) REVERT: F 455 MET cc_start: 0.8889 (tmm) cc_final: 0.8578 (tmm) REVERT: F 479 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8417 (pm20) outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 0.1838 time to fit residues: 12.2666 Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 401 HIS 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 9 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.060327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050940 restraints weight = 24276.611| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.38 r_work: 0.2835 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6799 Z= 0.356 Angle : 0.632 8.671 9239 Z= 0.329 Chirality : 0.045 0.269 1002 Planarity : 0.004 0.048 1181 Dihedral : 6.597 58.782 1114 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.71 % Allowed : 12.86 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.29), residues: 793 helix: 0.95 (0.28), residues: 383 sheet: 0.33 (0.77), residues: 39 loop : -1.65 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 165 HIS 0.004 0.001 HIS F 374 PHE 0.013 0.002 PHE F 369 TYR 0.015 0.002 TYR A 453 ARG 0.003 0.000 ARG F 460 *********************** 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 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 401 HIS cc_start: 0.8946 (OUTLIER) cc_final: 0.8591 (t-90) REVERT: F 455 MET cc_start: 0.8975 (tmm) cc_final: 0.8665 (tmm) REVERT: F 479 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8279 (pm20) outliers start: 12 outliers final: 5 residues processed: 51 average time/residue: 0.1870 time to fit residues: 13.5942 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 : 0.742 ------------------------------------------------------------------------------- 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 401 HIS Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 chunk 65 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.062770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.053264 restraints weight = 24145.877| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.46 r_work: 0.2896 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6799 Z= 0.158 Angle : 0.541 9.221 9239 Z= 0.278 Chirality : 0.041 0.250 1002 Planarity : 0.004 0.042 1181 Dihedral : 6.200 55.796 1114 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.30), residues: 793 helix: 1.17 (0.28), residues: 375 sheet: 0.60 (0.78), residues: 39 loop : -1.52 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.014 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 *********************** 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 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 365 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8396 (p) REVERT: F 401 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8368 (t-90) REVERT: F 455 MET cc_start: 0.8875 (tmm) cc_final: 0.8504 (tmm) REVERT: F 479 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8253 (pm20) outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 0.1742 time to fit residues: 13.5687 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 : 0.737 ------------------------------------------------------------------------------- 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 365 THR Chi-restraints excluded: chain F residue 401 HIS 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 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.063078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053664 restraints weight = 24116.588| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.43 r_work: 0.2903 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6799 Z= 0.157 Angle : 0.528 8.221 9239 Z= 0.270 Chirality : 0.041 0.258 1002 Planarity : 0.004 0.042 1181 Dihedral : 6.029 55.538 1114 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.14 % Allowed : 13.71 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.30), residues: 793 helix: 1.22 (0.28), residues: 376 sheet: 0.63 (0.78), residues: 42 loop : -1.44 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 493 PHE 0.013 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 *********************** 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 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 365 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8389 (p) REVERT: F 401 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8357 (t-90) REVERT: F 455 MET cc_start: 0.8920 (tmm) cc_final: 0.8538 (tmm) REVERT: F 479 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8265 (pm20) outliers start: 15 outliers final: 9 residues processed: 58 average time/residue: 0.1820 time to fit residues: 14.8263 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 434 ILE 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 252 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 401 HIS 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 12 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.062024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.052574 restraints weight = 24259.214| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.42 r_work: 0.2871 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6799 Z= 0.235 Angle : 0.572 8.148 9239 Z= 0.290 Chirality : 0.043 0.264 1002 Planarity : 0.004 0.040 1181 Dihedral : 6.117 56.944 1114 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.86 % Allowed : 14.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.30), residues: 793 helix: 1.17 (0.28), residues: 382 sheet: 0.87 (0.79), residues: 39 loop : -1.52 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 165 HIS 0.003 0.001 HIS F 374 PHE 0.012 0.001 PHE F 72 TYR 0.010 0.001 TYR F 50 ARG 0.002 0.000 ARG F 460 *********************** 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 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 365 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8481 (p) REVERT: F 401 HIS cc_start: 0.8813 (OUTLIER) cc_final: 0.8503 (t-90) REVERT: F 455 MET cc_start: 0.8951 (tmm) cc_final: 0.8579 (tmm) REVERT: F 479 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8297 (pm20) outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 0.1793 time to fit residues: 13.4663 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 : 0.747 ------------------------------------------------------------------------------- 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 518 LEU 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 365 THR Chi-restraints excluded: chain F residue 401 HIS 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 14 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.061367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051872 restraints weight = 24408.126| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.42 r_work: 0.2851 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6799 Z= 0.273 Angle : 0.599 8.323 9239 Z= 0.304 Chirality : 0.043 0.261 1002 Planarity : 0.004 0.041 1181 Dihedral : 6.251 57.619 1114 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.30), residues: 793 helix: 1.18 (0.28), residues: 382 sheet: 0.74 (0.79), residues: 39 loop : -1.60 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.012 0.001 PHE F 72 TYR 0.011 0.001 TYR A 453 ARG 0.002 0.000 ARG F 460 *********************** 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 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 365 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8543 (p) REVERT: F 401 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.8501 (t-90) REVERT: F 455 MET cc_start: 0.8953 (tmm) cc_final: 0.8590 (tmm) REVERT: F 479 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8255 (pm20) outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.1892 time to fit residues: 14.3122 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 518 LEU 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 365 THR Chi-restraints excluded: chain F residue 401 HIS 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 77 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 = 0.3240 r_free = 0.3240 target = 0.062408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052944 restraints weight = 24577.442| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.47 r_work: 0.2883 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6799 Z= 0.183 Angle : 0.561 8.024 9239 Z= 0.283 Chirality : 0.042 0.255 1002 Planarity : 0.004 0.042 1181 Dihedral : 6.080 56.140 1114 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 793 helix: 1.36 (0.28), residues: 375 sheet: 0.90 (0.81), residues: 39 loop : -1.55 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.003 0.001 HIS F 493 PHE 0.013 0.001 PHE F 72 TYR 0.010 0.001 TYR F 50 ARG 0.002 0.000 ARG F 273 ********************** 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 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 365 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8566 (p) REVERT: F 401 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8420 (t-90) REVERT: F 455 MET cc_start: 0.8888 (tmm) cc_final: 0.8479 (tmm) REVERT: F 479 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8252 (pm20) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.1807 time to fit residues: 13.7484 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 252 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 401 HIS 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 51 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.061847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.052376 restraints weight = 24521.574| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.44 r_work: 0.2867 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6799 Z= 0.229 Angle : 0.579 8.049 9239 Z= 0.292 Chirality : 0.042 0.261 1002 Planarity : 0.004 0.044 1181 Dihedral : 6.117 56.657 1114 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.57 % Allowed : 15.43 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 793 helix: 1.34 (0.28), residues: 376 sheet: 0.98 (0.82), residues: 39 loop : -1.56 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.012 0.001 PHE F 72 TYR 0.010 0.001 TYR F 50 ARG 0.002 0.000 ARG F 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.94 seconds wall clock time: 59 minutes 59.21 seconds (3599.21 seconds total)