Starting phenix.real_space_refine on Tue Mar 11 18:01:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo6_33338/03_2025/7xo6_33338.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo6_33338/03_2025/7xo6_33338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo6_33338/03_2025/7xo6_33338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo6_33338/03_2025/7xo6_33338.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo6_33338/03_2025/7xo6_33338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo6_33338/03_2025/7xo6_33338.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4112 2.51 5 N 1076 2.21 5 O 1214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6440 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "A" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "B" 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.43, per 1000 atoms: 0.84 Number of scatterers: 6440 At special positions: 0 Unit cell: (97.232, 74.984, 121.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1214 8.00 N 1076 7.00 C 4112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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-ASN " NAG A1301 " - " ASN A 343 " " NAG B 1 " - " ASN D 53 " " NAG D 902 " - " ASN D 546 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 904.4 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 56.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'D' and resid 22 through 53 removed outlier: 4.023A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.671A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.705A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.964A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 250 removed outlier: 3.769A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.521A pdb=" N ARG D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.626A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.653A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.637A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.516A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.468A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.719A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.514A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.514A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.705A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.265A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.858A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.935A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.798A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.595A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 831 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: 1.68 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1188 1.33 - 1.45: 1836 1.45 - 1.57: 3536 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6618 Sorted by residual: bond pdb=" CA SER A 349 " pdb=" CB SER A 349 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.61e-02 3.86e+03 1.93e+01 bond pdb=" C ALA A 348 " pdb=" N SER A 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.31e-02 5.83e+03 6.32e+00 bond pdb=" CA ALA A 348 " pdb=" CB ALA A 348 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.66e-02 3.63e+03 5.69e+00 bond pdb=" C PRO A 373 " pdb=" O PRO A 373 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.30e-02 5.92e+03 4.91e+00 bond pdb=" CA ALA A 348 " pdb=" C ALA A 348 " ideal model delta sigma weight residual 1.526 1.498 0.029 1.37e-02 5.33e+03 4.38e+00 ... (remaining 6613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 8894 2.40 - 4.79: 80 4.79 - 7.19: 8 7.19 - 9.58: 3 9.58 - 11.98: 2 Bond angle restraints: 8987 Sorted by residual: angle pdb=" N PRO D 289 " pdb=" CA PRO D 289 " pdb=" C PRO D 289 " ideal model delta sigma weight residual 112.47 121.13 -8.66 2.06e+00 2.36e-01 1.77e+01 angle pdb=" C3 NAG B 1 " pdb=" C2 NAG B 1 " pdb=" N2 NAG B 1 " ideal model delta sigma weight residual 110.74 98.76 11.98 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CA SER A 349 " pdb=" C SER A 349 " pdb=" O SER A 349 " ideal model delta sigma weight residual 121.87 117.48 4.39 1.16e+00 7.43e-01 1.43e+01 angle pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " pdb=" CD2 LEU A 518 " ideal model delta sigma weight residual 110.70 120.82 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " pdb=" CD1 LEU A 518 " ideal model delta sigma weight residual 110.70 120.26 -9.56 3.00e+00 1.11e-01 1.02e+01 ... (remaining 8982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3624 17.64 - 35.29: 251 35.29 - 52.93: 50 52.93 - 70.57: 15 70.57 - 88.22: 8 Dihedral angle restraints: 3948 sinusoidal: 1635 harmonic: 2313 Sorted by residual: dihedral pdb=" C ASP A 339 " pdb=" N ASP A 339 " pdb=" CA ASP A 339 " pdb=" CB ASP A 339 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" C GLN D 287 " pdb=" N GLN D 287 " pdb=" CA GLN D 287 " pdb=" CB GLN D 287 " ideal model delta harmonic sigma weight residual -122.60 -131.90 9.30 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" N PRO D 289 " pdb=" C PRO D 289 " pdb=" CA PRO D 289 " pdb=" CB PRO D 289 " ideal model delta harmonic sigma weight residual 115.10 124.08 -8.98 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 3945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 941 0.338 - 0.675: 3 0.675 - 1.013: 0 1.013 - 1.350: 1 1.350 - 1.688: 1 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.19e+01 chirality pdb=" CG LEU A 518 " pdb=" CB LEU A 518 " pdb=" CD1 LEU A 518 " pdb=" CD2 LEU A 518 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.12e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 943 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.266 2.00e-02 2.50e+03 2.22e-01 6.14e+02 pdb=" C7 NAG A1301 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.369 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.189 2.00e-02 2.50e+03 1.53e-01 2.92e+02 pdb=" C7 NAG B 2 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.240 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 902 " 0.159 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG D 902 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG D 902 " 0.117 2.00e-02 2.50e+03 pdb=" N2 NAG D 902 " -0.218 2.00e-02 2.50e+03 pdb=" O7 NAG D 902 " -0.014 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 80 2.64 - 3.21: 5947 3.21 - 3.77: 10011 3.77 - 4.34: 13887 4.34 - 4.90: 23217 Nonbonded interactions: 53142 Sorted by model distance: nonbonded pdb=" OH TYR D 279 " pdb=" OD1 ASN D 290 " model vdw 2.075 3.040 nonbonded pdb=" OG1 THR D 365 " pdb=" OD1 ASN D 368 " model vdw 2.146 3.040 nonbonded pdb=" OD2 ASP D 494 " pdb=" OG1 THR D 496 " model vdw 2.156 3.040 nonbonded pdb=" NH1 ARG D 177 " pdb=" O GLU D 495 " model vdw 2.221 3.120 nonbonded pdb=" O ALA D 212 " pdb=" ND2 ASN D 216 " model vdw 2.269 3.120 ... (remaining 53137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.100 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.010 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 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 0.071 6618 Z= 0.179 Angle : 0.556 11.980 8987 Z= 0.286 Chirality : 0.080 1.688 946 Planarity : 0.009 0.222 1160 Dihedral : 13.228 88.216 2462 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.28), residues: 780 helix: -0.11 (0.25), residues: 385 sheet: -0.50 (0.74), residues: 41 loop : -1.95 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP D 163 HIS 0.002 0.000 HIS A 519 PHE 0.016 0.001 PHE A 374 TYR 0.005 0.000 TYR A 495 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.677 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 212 average time/residue: 1.1163 time to fit residues: 248.9809 Evaluate side-chains 156 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 421 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.0050 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.0070 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 86 GLN D 101 GLN D 197 ASN D 221 GLN D 265 HIS D 368 ASN D 373 HIS D 378 HIS D 524 GLN D 552 GLN D 562 ASN D 598 GLN D 599 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.132993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.122422 restraints weight = 9183.154| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.65 r_work: 0.3659 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6618 Z= 0.278 Angle : 0.576 5.214 8987 Z= 0.294 Chirality : 0.045 0.161 946 Planarity : 0.004 0.046 1160 Dihedral : 4.829 41.698 949 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.65 % Allowed : 19.27 % Favored : 77.08 % 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: -0.23 (0.29), residues: 780 helix: 0.86 (0.26), residues: 387 sheet: -0.19 (0.67), residues: 41 loop : -1.31 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 163 HIS 0.006 0.001 HIS D 373 PHE 0.015 0.002 PHE D 72 TYR 0.022 0.002 TYR D 202 ARG 0.008 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.705 Fit side-chains REVERT: D 206 ASP cc_start: 0.7611 (t0) cc_final: 0.6616 (t0) REVERT: D 249 MET cc_start: 0.8417 (mmm) cc_final: 0.7959 (mpp) REVERT: D 369 PHE cc_start: 0.8049 (t80) cc_final: 0.7797 (t80) REVERT: D 497 TYR cc_start: 0.8465 (m-80) cc_final: 0.8254 (m-80) REVERT: D 517 THR cc_start: 0.7891 (p) cc_final: 0.7607 (p) REVERT: A 355 ARG cc_start: 0.8105 (tpp-160) cc_final: 0.7847 (ttt90) REVERT: A 477 ASN cc_start: 0.7820 (t0) cc_final: 0.7423 (t0) outliers start: 25 outliers final: 8 residues processed: 169 average time/residue: 1.2401 time to fit residues: 219.7259 Evaluate side-chains 159 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 28 optimal weight: 0.0470 chunk 7 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN D 531 GLN D 578 ASN A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 450 ASN A 505 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.133512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122945 restraints weight = 9233.457| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.67 r_work: 0.3671 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6618 Z= 0.181 Angle : 0.517 9.638 8987 Z= 0.259 Chirality : 0.041 0.142 946 Planarity : 0.004 0.043 1160 Dihedral : 4.338 36.435 945 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.07 % Allowed : 22.63 % Favored : 74.31 % 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 (0.29), residues: 780 helix: 1.22 (0.26), residues: 386 sheet: 0.02 (0.68), residues: 43 loop : -1.05 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.012 0.001 PHE D 285 TYR 0.020 0.001 TYR D 202 ARG 0.005 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.676 Fit side-chains REVERT: D 102 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: D 183 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7919 (t80) REVERT: D 323 MET cc_start: 0.7978 (mmm) cc_final: 0.7762 (mmt) REVERT: D 369 PHE cc_start: 0.8030 (t80) cc_final: 0.7701 (t80) REVERT: D 497 TYR cc_start: 0.8467 (m-80) cc_final: 0.8218 (m-80) REVERT: D 517 THR cc_start: 0.7788 (p) cc_final: 0.7489 (p) REVERT: A 355 ARG cc_start: 0.8085 (tpp-160) cc_final: 0.7783 (ttt90) REVERT: A 477 ASN cc_start: 0.7888 (t0) cc_final: 0.7614 (t160) REVERT: A 496 SER cc_start: 0.7164 (OUTLIER) cc_final: 0.6940 (p) outliers start: 21 outliers final: 7 residues processed: 158 average time/residue: 1.2767 time to fit residues: 211.6620 Evaluate side-chains 156 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 496 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 0.0770 chunk 30 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 overall best weight: 0.0892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN D 524 GLN D 531 GLN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.138473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.127883 restraints weight = 9281.268| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.70 r_work: 0.3689 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6618 Z= 0.131 Angle : 0.471 7.046 8987 Z= 0.237 Chirality : 0.039 0.135 946 Planarity : 0.004 0.041 1160 Dihedral : 3.993 35.279 945 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.92 % Allowed : 23.36 % Favored : 73.72 % 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: 0.65 (0.30), residues: 780 helix: 1.56 (0.27), residues: 381 sheet: 0.13 (0.70), residues: 43 loop : -0.77 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.008 0.001 PHE D 285 TYR 0.022 0.001 TYR D 202 ARG 0.003 0.000 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.665 Fit side-chains REVERT: D 176 LEU cc_start: 0.8453 (mt) cc_final: 0.8250 (mt) REVERT: D 323 MET cc_start: 0.7952 (mmm) cc_final: 0.7541 (mmm) REVERT: D 369 PHE cc_start: 0.7960 (t80) cc_final: 0.7649 (t80) REVERT: D 497 TYR cc_start: 0.8444 (m-80) cc_final: 0.8196 (m-80) REVERT: D 517 THR cc_start: 0.7559 (p) cc_final: 0.7232 (p) REVERT: A 365 TYR cc_start: 0.7313 (m-80) cc_final: 0.7056 (m-80) REVERT: A 477 ASN cc_start: 0.7858 (t0) cc_final: 0.7589 (t160) outliers start: 20 outliers final: 9 residues processed: 156 average time/residue: 1.1905 time to fit residues: 195.2329 Evaluate side-chains 153 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 501 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 10 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 chunk 21 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 30 optimal weight: 0.0980 chunk 73 optimal weight: 0.0060 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN D 472 GLN D 524 GLN D 531 GLN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.136371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.125845 restraints weight = 9207.061| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.70 r_work: 0.3683 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6618 Z= 0.168 Angle : 0.484 7.028 8987 Z= 0.245 Chirality : 0.040 0.134 946 Planarity : 0.004 0.041 1160 Dihedral : 3.949 33.259 945 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.21 % Allowed : 23.65 % Favored : 73.14 % 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: 0.80 (0.30), residues: 780 helix: 1.62 (0.27), residues: 387 sheet: 0.17 (0.71), residues: 43 loop : -0.66 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 69 HIS 0.004 0.001 HIS D 374 PHE 0.009 0.001 PHE D 592 TYR 0.022 0.001 TYR D 202 ARG 0.007 0.001 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.727 Fit side-chains REVERT: D 323 MET cc_start: 0.8018 (mmm) cc_final: 0.7651 (mmm) REVERT: D 369 PHE cc_start: 0.7982 (t80) cc_final: 0.7632 (t80) REVERT: D 497 TYR cc_start: 0.8455 (m-80) cc_final: 0.8239 (m-80) REVERT: D 517 THR cc_start: 0.7718 (p) cc_final: 0.7360 (p) REVERT: A 355 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7817 (ttt90) REVERT: A 365 TYR cc_start: 0.7344 (m-80) cc_final: 0.7024 (m-80) REVERT: A 396 TYR cc_start: 0.7524 (m-80) cc_final: 0.7308 (m-80) REVERT: A 477 ASN cc_start: 0.7862 (t0) cc_final: 0.7585 (t160) REVERT: A 496 SER cc_start: 0.7146 (OUTLIER) cc_final: 0.6906 (p) outliers start: 22 outliers final: 11 residues processed: 163 average time/residue: 1.2262 time to fit residues: 209.6862 Evaluate side-chains 162 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 501 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 0.0970 chunk 10 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 77 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 524 GLN D 531 GLN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.135597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.125224 restraints weight = 9077.156| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.68 r_work: 0.3648 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6618 Z= 0.202 Angle : 0.508 7.474 8987 Z= 0.255 Chirality : 0.040 0.132 946 Planarity : 0.004 0.043 1160 Dihedral : 4.078 31.995 945 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.07 % Allowed : 24.23 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.30), residues: 780 helix: 1.58 (0.27), residues: 394 sheet: 0.25 (0.71), residues: 43 loop : -0.66 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.004 0.001 HIS D 374 PHE 0.009 0.001 PHE D 523 TYR 0.022 0.002 TYR D 202 ARG 0.008 0.001 ARG D 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.728 Fit side-chains REVERT: D 323 MET cc_start: 0.8017 (mmm) cc_final: 0.7621 (mmm) REVERT: D 369 PHE cc_start: 0.7964 (t80) cc_final: 0.7576 (t80) REVERT: D 497 TYR cc_start: 0.8470 (m-80) cc_final: 0.8264 (m-80) REVERT: D 517 THR cc_start: 0.7777 (p) cc_final: 0.7467 (p) REVERT: A 355 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7837 (ttt90) REVERT: A 365 TYR cc_start: 0.7362 (m-80) cc_final: 0.7080 (m-80) REVERT: A 396 TYR cc_start: 0.7527 (m-80) cc_final: 0.7308 (m-80) REVERT: A 477 ASN cc_start: 0.7852 (t0) cc_final: 0.7584 (t160) REVERT: A 496 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6883 (p) outliers start: 21 outliers final: 8 residues processed: 158 average time/residue: 1.2214 time to fit residues: 202.4570 Evaluate side-chains 155 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 496 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.2980 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 63 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN D 531 GLN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.135583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125083 restraints weight = 9142.865| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.70 r_work: 0.3669 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6618 Z= 0.183 Angle : 0.517 10.610 8987 Z= 0.258 Chirality : 0.040 0.131 946 Planarity : 0.004 0.044 1160 Dihedral : 4.078 30.993 945 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.63 % Allowed : 25.55 % Favored : 71.82 % 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: 0.87 (0.31), residues: 780 helix: 1.65 (0.27), residues: 394 sheet: 0.24 (0.72), residues: 43 loop : -0.63 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.004 0.001 HIS D 322 PHE 0.013 0.001 PHE D 83 TYR 0.023 0.001 TYR D 202 ARG 0.008 0.001 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.676 Fit side-chains REVERT: D 183 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7830 (t80) REVERT: D 369 PHE cc_start: 0.7946 (t80) cc_final: 0.7532 (t80) REVERT: D 497 TYR cc_start: 0.8477 (m-80) cc_final: 0.8273 (m-80) REVERT: D 517 THR cc_start: 0.7760 (p) cc_final: 0.7470 (p) REVERT: A 355 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7822 (ttt90) REVERT: A 365 TYR cc_start: 0.7411 (m-80) cc_final: 0.7120 (m-80) REVERT: A 396 TYR cc_start: 0.7568 (m-80) cc_final: 0.7340 (m-80) REVERT: A 477 ASN cc_start: 0.7856 (t0) cc_final: 0.7579 (t160) outliers start: 18 outliers final: 9 residues processed: 156 average time/residue: 1.5163 time to fit residues: 246.3906 Evaluate side-chains 159 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.6980 chunk 71 optimal weight: 0.0050 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 27 optimal weight: 0.2980 chunk 47 optimal weight: 0.0670 chunk 45 optimal weight: 0.2980 chunk 54 optimal weight: 0.1980 overall best weight: 0.1532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN D 531 GLN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.136250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.125656 restraints weight = 9182.708| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.71 r_work: 0.3667 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6618 Z= 0.161 Angle : 0.510 10.074 8987 Z= 0.254 Chirality : 0.039 0.130 946 Planarity : 0.004 0.041 1160 Dihedral : 3.933 29.305 945 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.61 % Allowed : 26.86 % Favored : 71.53 % 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: 0.97 (0.31), residues: 780 helix: 1.74 (0.27), residues: 394 sheet: 0.28 (0.72), residues: 43 loop : -0.59 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.004 0.001 HIS D 374 PHE 0.009 0.001 PHE D 327 TYR 0.023 0.001 TYR D 202 ARG 0.010 0.001 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: D 183 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7812 (t80) REVERT: D 331 SER cc_start: 0.8341 (p) cc_final: 0.8135 (p) REVERT: D 369 PHE cc_start: 0.7928 (t80) cc_final: 0.7490 (t80) REVERT: D 497 TYR cc_start: 0.8480 (m-80) cc_final: 0.8276 (m-80) REVERT: D 517 THR cc_start: 0.7729 (p) cc_final: 0.7389 (p) REVERT: A 355 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7830 (ttt90) REVERT: A 365 TYR cc_start: 0.7406 (m-80) cc_final: 0.7100 (m-80) REVERT: A 396 TYR cc_start: 0.7567 (m-80) cc_final: 0.7365 (m-80) REVERT: A 477 ASN cc_start: 0.7833 (t0) cc_final: 0.7562 (t160) REVERT: A 509 ARG cc_start: 0.8636 (mtt180) cc_final: 0.8433 (mtt-85) outliers start: 11 outliers final: 6 residues processed: 151 average time/residue: 1.2700 time to fit residues: 200.9704 Evaluate side-chains 157 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 26 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN D 531 GLN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.133823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123282 restraints weight = 9220.223| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.69 r_work: 0.3644 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6618 Z= 0.252 Angle : 0.552 9.377 8987 Z= 0.277 Chirality : 0.042 0.132 946 Planarity : 0.004 0.044 1160 Dihedral : 4.264 27.798 945 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.46 % Allowed : 26.72 % Favored : 71.82 % 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: 0.74 (0.30), residues: 780 helix: 1.52 (0.27), residues: 388 sheet: 0.24 (0.71), residues: 43 loop : -0.63 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 477 HIS 0.004 0.001 HIS D 374 PHE 0.014 0.001 PHE D 83 TYR 0.023 0.002 TYR D 202 ARG 0.010 0.001 ARG D 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: D 183 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7595 (t80) REVERT: D 297 MET cc_start: 0.8484 (mtm) cc_final: 0.8098 (mtp) REVERT: A 355 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7820 (ttt90) REVERT: A 365 TYR cc_start: 0.7416 (m-80) cc_final: 0.7090 (m-80) REVERT: A 477 ASN cc_start: 0.7869 (t0) cc_final: 0.7595 (t160) outliers start: 10 outliers final: 5 residues processed: 157 average time/residue: 1.3452 time to fit residues: 221.4671 Evaluate side-chains 154 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.0170 chunk 51 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN D 397 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.134237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.123747 restraints weight = 9232.719| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.69 r_work: 0.3642 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6618 Z= 0.267 Angle : 0.566 9.423 8987 Z= 0.282 Chirality : 0.042 0.132 946 Planarity : 0.004 0.048 1160 Dihedral : 4.438 27.180 945 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.46 % Allowed : 27.30 % Favored : 71.24 % 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: 0.59 (0.30), residues: 780 helix: 1.34 (0.27), residues: 394 sheet: 0.22 (0.72), residues: 43 loop : -0.67 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.006 0.001 HIS D 322 PHE 0.011 0.001 PHE D 327 TYR 0.024 0.002 TYR D 202 ARG 0.013 0.001 ARG D 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: D 183 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7615 (t80) REVERT: D 297 MET cc_start: 0.8473 (mtm) cc_final: 0.8240 (mtp) REVERT: D 609 GLU cc_start: 0.7474 (mp0) cc_final: 0.7230 (mp0) REVERT: A 355 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7814 (ttt90) REVERT: A 365 TYR cc_start: 0.7443 (m-80) cc_final: 0.7118 (m-80) REVERT: A 477 ASN cc_start: 0.7899 (t0) cc_final: 0.7697 (t0) outliers start: 10 outliers final: 5 residues processed: 152 average time/residue: 1.2348 time to fit residues: 196.7853 Evaluate side-chains 162 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 35 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.0670 chunk 67 optimal weight: 0.2980 chunk 7 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 overall best weight: 0.1634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN D 397 ASN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.135669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125176 restraints weight = 9258.235| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.70 r_work: 0.3670 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6618 Z= 0.172 Angle : 0.532 9.588 8987 Z= 0.265 Chirality : 0.040 0.129 946 Planarity : 0.004 0.052 1160 Dihedral : 4.097 26.640 945 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.31 % Allowed : 27.74 % Favored : 70.95 % 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: 0.78 (0.31), residues: 780 helix: 1.52 (0.27), residues: 394 sheet: 0.26 (0.71), residues: 43 loop : -0.61 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 69 HIS 0.004 0.001 HIS D 322 PHE 0.010 0.001 PHE D 327 TYR 0.024 0.001 TYR D 202 ARG 0.013 0.001 ARG D 577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6425.52 seconds wall clock time: 109 minutes 42.51 seconds (6582.51 seconds total)