Starting phenix.real_space_refine on Tue Jan 14 00:20:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1n_37997/01_2025/8x1n_37997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1n_37997/01_2025/8x1n_37997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x1n_37997/01_2025/8x1n_37997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1n_37997/01_2025/8x1n_37997.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1n_37997/01_2025/8x1n_37997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1n_37997/01_2025/8x1n_37997.cif" } resolution = 3.31 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= 0.047 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 40 5.16 5 C 3008 2.51 5 N 792 2.21 5 O 922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4763 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4651 Classifications: {'peptide': 591} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 569} 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: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {' ZN': 1, 'PLM': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.51, per 1000 atoms: 0.74 Number of scatterers: 4763 At special positions: 0 Unit cell: (70.484, 93.628, 103.096, 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 40 16.00 O 922 8.00 N 792 7.00 C 3008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.04 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.04 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " 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-ASN " NAG B 1 " - " ASN A 251 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 566.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 268 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 264 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 22 " 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 59 through 75 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.729A pdb=" N CYS A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.762A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 146 through 154 removed outlier: 4.292A pdb=" N GLU A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.894A pdb=" N ARG A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 193 removed outlier: 3.525A pdb=" N ILE A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 197 through 247 removed outlier: 3.788A pdb=" N ALA A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ARG A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 271 removed outlier: 3.855A pdb=" N LYS A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 removed outlier: 3.546A pdb=" N GLN A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.515A pdb=" N THR A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 343 through 362 removed outlier: 3.911A pdb=" N ARG A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.534A pdb=" N PHE A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.586A pdb=" N CYS A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.611A pdb=" N GLN A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 439 Processing helix chain 'A' and resid 443 through 462 removed outlier: 3.813A pdb=" N CYS A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 491 removed outlier: 4.103A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.924A pdb=" N CYS A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 513 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.759A pdb=" N ILE A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.687A pdb=" N GLN A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 removed outlier: 3.812A pdb=" N PHE A 552 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 584 removed outlier: 4.165A pdb=" N GLN A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.452A pdb=" N GLN A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 879 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: 1.20 Time building geometry restraints manager: 1.48 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: 1570 1.35 - 1.47: 1031 1.47 - 1.59: 2193 1.59 - 1.71: 0 1.71 - 1.83: 48 Bond restraints: 4842 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1 PLM A 704 " pdb=" C2 PLM A 704 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 PLM A 703 " pdb=" C2 PLM A 703 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.45e+00 ... (remaining 4837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 6345 1.53 - 3.06: 133 3.06 - 4.60: 27 4.60 - 6.13: 5 6.13 - 7.66: 3 Bond angle restraints: 6513 Sorted by residual: angle pdb=" CA CYS A 472 " pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " ideal model delta sigma weight residual 114.40 121.49 -7.09 2.30e+00 1.89e-01 9.50e+00 angle pdb=" N CYS A 461 " pdb=" CA CYS A 461 " pdb=" C CYS A 461 " ideal model delta sigma weight residual 111.71 115.70 -3.99 1.34e+00 5.57e-01 8.88e+00 angle pdb=" N CYS A 462 " pdb=" CA CYS A 462 " pdb=" C CYS A 462 " ideal model delta sigma weight residual 113.01 109.47 3.54 1.20e+00 6.94e-01 8.70e+00 angle pdb=" CA GLN A 291 " pdb=" C GLN A 291 " pdb=" N GLN A 292 " ideal model delta sigma weight residual 114.76 117.84 -3.08 1.14e+00 7.69e-01 7.30e+00 angle pdb=" CB MET A 159 " pdb=" CG MET A 159 " pdb=" SD MET A 159 " ideal model delta sigma weight residual 112.70 120.36 -7.66 3.00e+00 1.11e-01 6.52e+00 ... (remaining 6508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 2802 22.13 - 44.27: 221 44.27 - 66.40: 31 66.40 - 88.53: 14 88.53 - 110.66: 7 Dihedral angle restraints: 3075 sinusoidal: 1338 harmonic: 1737 Sorted by residual: dihedral pdb=" CB CYS A 461 " pdb=" SG CYS A 461 " pdb=" SG CYS A 472 " pdb=" CB CYS A 472 " ideal model delta sinusoidal sigma weight residual -86.00 -176.31 90.31 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 583 " pdb=" CB CYS A 583 " ideal model delta sinusoidal sigma weight residual -86.00 -169.00 83.00 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual -86.00 -167.52 81.52 1 1.00e+01 1.00e-02 8.18e+01 ... (remaining 3072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 638 0.056 - 0.111: 87 0.111 - 0.167: 6 0.167 - 0.223: 0 0.223 - 0.278: 2 Chirality restraints: 733 Sorted by residual: 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 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 251 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA CYS A 461 " pdb=" N CYS A 461 " pdb=" C CYS A 461 " pdb=" CB CYS A 461 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 730 not shown) Planarity restraints: 843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 132 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 133 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 494 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 495 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 336 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C ASP A 336 " -0.018 2.00e-02 2.50e+03 pdb=" O ASP A 336 " 0.007 2.00e-02 2.50e+03 pdb=" N ARG A 337 " 0.006 2.00e-02 2.50e+03 ... (remaining 840 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1013 2.78 - 3.31: 4403 3.31 - 3.84: 7369 3.84 - 4.37: 7898 4.37 - 4.90: 14920 Nonbonded interactions: 35603 Sorted by model distance: nonbonded pdb=" O SER A 34 " pdb=" OG SER A 34 " model vdw 2.251 3.040 nonbonded pdb=" ND2 ASN A 329 " pdb=" OD1 ASN A 331 " model vdw 2.285 3.120 nonbonded pdb=" OE2 GLU A 392 " pdb=" NZ LYS A 396 " model vdw 2.326 3.120 nonbonded pdb=" O LEU A 432 " pdb=" OG1 THR A 436 " model vdw 2.352 3.040 nonbonded pdb=" O GLU A 88 " pdb=" NE2 GLN A 90 " model vdw 2.395 3.120 ... (remaining 35598 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: 0.510 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 0.051 4842 Z= 0.204 Angle : 0.594 7.660 6513 Z= 0.327 Chirality : 0.040 0.278 733 Planarity : 0.003 0.041 842 Dihedral : 16.855 110.663 1897 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.36), residues: 589 helix: 1.99 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -0.01 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.004 0.001 HIS A 268 PHE 0.010 0.001 PHE A 339 TYR 0.010 0.001 TYR A 435 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.569 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2221 time to fit residues: 13.1555 Evaluate side-chains 46 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.168491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124802 restraints weight = 5351.564| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.23 r_work: 0.3212 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4842 Z= 0.150 Angle : 0.481 6.170 6513 Z= 0.251 Chirality : 0.038 0.182 733 Planarity : 0.003 0.039 842 Dihedral : 9.149 58.949 747 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.94 % Allowed : 10.87 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.36), residues: 589 helix: 2.08 (0.26), residues: 407 sheet: None (None), residues: 0 loop : -0.30 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.004 0.001 HIS A 268 PHE 0.008 0.001 PHE A 575 TYR 0.010 0.001 TYR A 435 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.552 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.1878 time to fit residues: 14.2924 Evaluate side-chains 53 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 472 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.168272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124445 restraints weight = 5332.152| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.23 r_work: 0.3165 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4842 Z= 0.163 Angle : 0.465 5.875 6513 Z= 0.242 Chirality : 0.038 0.190 733 Planarity : 0.003 0.041 842 Dihedral : 7.394 58.203 747 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.52 % Allowed : 11.84 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.36), residues: 589 helix: 2.09 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.28 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.004 0.001 HIS A 268 PHE 0.008 0.001 PHE A 575 TYR 0.010 0.001 TYR A 151 ARG 0.001 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6610 (pt0) outliers start: 13 outliers final: 9 residues processed: 58 average time/residue: 0.1956 time to fit residues: 14.5666 Evaluate side-chains 51 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.170121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.127025 restraints weight = 5370.653| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.21 r_work: 0.3061 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4842 Z= 0.197 Angle : 0.471 6.822 6513 Z= 0.246 Chirality : 0.038 0.192 733 Planarity : 0.003 0.040 842 Dihedral : 6.970 58.685 747 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.52 % Allowed : 12.43 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.36), residues: 589 helix: 2.13 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.24 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.004 0.001 HIS A 483 PHE 0.008 0.001 PHE A 575 TYR 0.009 0.001 TYR A 425 ARG 0.001 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6127 (pt0) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.1834 time to fit residues: 13.5883 Evaluate side-chains 55 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 386 GLN A 597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.175835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131714 restraints weight = 5458.706| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.31 r_work: 0.2897 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 4842 Z= 0.150 Angle : 0.440 5.295 6513 Z= 0.231 Chirality : 0.037 0.186 733 Planarity : 0.003 0.040 842 Dihedral : 6.658 59.609 747 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.14 % Allowed : 13.20 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.36), residues: 589 helix: 2.21 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.36 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.003 0.001 HIS A 483 PHE 0.006 0.001 PHE A 575 TYR 0.008 0.001 TYR A 426 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 329 ASN cc_start: 0.8237 (p0) cc_final: 0.8008 (p0) REVERT: A 331 ASN cc_start: 0.8433 (m110) cc_final: 0.8119 (p0) REVERT: A 400 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6427 (pt0) REVERT: A 511 CYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5671 (t) outliers start: 11 outliers final: 9 residues processed: 55 average time/residue: 0.1770 time to fit residues: 12.8245 Evaluate side-chains 55 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.0050 chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.0000 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 331 ASN A 483 HIS A 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.174209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131176 restraints weight = 5403.863| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.27 r_work: 0.3199 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4842 Z= 0.134 Angle : 0.417 5.610 6513 Z= 0.218 Chirality : 0.036 0.184 733 Planarity : 0.003 0.040 842 Dihedral : 6.399 59.955 747 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.33 % Allowed : 13.59 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.36), residues: 589 helix: 2.38 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.37 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 181 HIS 0.003 0.001 HIS A 483 PHE 0.006 0.001 PHE A 512 TYR 0.008 0.001 TYR A 151 ARG 0.001 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6717 (pt0) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.1879 time to fit residues: 13.4000 Evaluate side-chains 53 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.174778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130739 restraints weight = 5335.348| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.27 r_work: 0.3241 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4842 Z= 0.176 Angle : 0.442 6.413 6513 Z= 0.231 Chirality : 0.037 0.196 733 Planarity : 0.003 0.041 842 Dihedral : 6.601 59.667 747 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.33 % Allowed : 14.37 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.36), residues: 589 helix: 2.35 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.32 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.003 0.001 HIS A 268 PHE 0.008 0.001 PHE A 385 TYR 0.008 0.001 TYR A 426 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6780 (pt0) outliers start: 12 outliers final: 11 residues processed: 58 average time/residue: 0.1731 time to fit residues: 13.1334 Evaluate side-chains 57 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131759 restraints weight = 5387.833| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.25 r_work: 0.3069 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4842 Z= 0.179 Angle : 0.459 6.797 6513 Z= 0.240 Chirality : 0.037 0.194 733 Planarity : 0.003 0.040 842 Dihedral : 6.702 59.602 747 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.91 % Allowed : 14.37 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.36), residues: 589 helix: 2.37 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.33 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.003 0.001 HIS A 268 PHE 0.009 0.001 PHE A 385 TYR 0.009 0.001 TYR A 151 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6572 (pt0) outliers start: 15 outliers final: 14 residues processed: 55 average time/residue: 0.1699 time to fit residues: 12.3365 Evaluate side-chains 60 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.176116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132435 restraints weight = 5386.858| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.26 r_work: 0.3031 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 4842 Z= 0.161 Angle : 0.447 7.443 6513 Z= 0.234 Chirality : 0.037 0.193 733 Planarity : 0.003 0.040 842 Dihedral : 6.692 59.548 747 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.91 % Allowed : 14.37 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.36), residues: 589 helix: 2.41 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.30 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 181 HIS 0.003 0.001 HIS A 268 PHE 0.007 0.001 PHE A 385 TYR 0.007 0.001 TYR A 426 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7884 (ptp-110) REVERT: A 400 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6436 (pt0) outliers start: 15 outliers final: 14 residues processed: 56 average time/residue: 0.1834 time to fit residues: 13.4738 Evaluate side-chains 61 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.175002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.131037 restraints weight = 5349.079| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.28 r_work: 0.3064 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4842 Z= 0.178 Angle : 0.502 15.453 6513 Z= 0.256 Chirality : 0.038 0.222 733 Planarity : 0.003 0.040 842 Dihedral : 6.800 59.474 747 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.72 % Allowed : 13.79 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.36), residues: 589 helix: 2.36 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.29 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.003 0.001 HIS A 268 PHE 0.008 0.001 PHE A 385 TYR 0.012 0.001 TYR A 151 ARG 0.001 0.000 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.8618 (m110) cc_final: 0.8416 (p0) REVERT: A 400 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6651 (pt0) outliers start: 14 outliers final: 14 residues processed: 56 average time/residue: 0.1773 time to fit residues: 13.0082 Evaluate side-chains 60 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.172594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.128573 restraints weight = 5416.150| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.27 r_work: 0.3124 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4842 Z= 0.207 Angle : 0.505 14.175 6513 Z= 0.259 Chirality : 0.039 0.214 733 Planarity : 0.003 0.040 842 Dihedral : 6.808 57.733 747 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.72 % Allowed : 13.98 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.36), residues: 589 helix: 2.25 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.34 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.004 0.001 HIS A 268 PHE 0.009 0.001 PHE A 385 TYR 0.009 0.001 TYR A 425 ARG 0.001 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.73 seconds wall clock time: 42 minutes 3.71 seconds (2523.71 seconds total)