Starting phenix.real_space_refine on Tue Mar 3 15:36:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsa_32752/03_2026/7wsa_32752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsa_32752/03_2026/7wsa_32752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wsa_32752/03_2026/7wsa_32752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsa_32752/03_2026/7wsa_32752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wsa_32752/03_2026/7wsa_32752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsa_32752/03_2026/7wsa_32752.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4203 2.51 5 N 1084 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6567 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} 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 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.46, per 1000 atoms: 0.22 Number of scatterers: 6567 At special positions: 0 Unit cell: (74.048, 93.184, 121.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1243 8.00 N 1084 7.00 C 4203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 243.7 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 56.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.896A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.599A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.725A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 52 removed outlier: 3.507A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.281A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.661A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.782A 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 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.339A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix 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 removed outlier: 3.851A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.537A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.849A 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: 3.862A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.671A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.354A 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 removed outlier: 3.669A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.434A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.832A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.531A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.987A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.164A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1964 1.34 - 1.46: 1406 1.46 - 1.58: 3324 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6752 Sorted by residual: bond pdb=" CA ALA D 36 " pdb=" CB ALA D 36 " ideal model delta sigma weight residual 1.532 1.485 0.047 1.57e-02 4.06e+03 8.94e+00 bond pdb=" N VAL D 488 " pdb=" CA VAL D 488 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.24e-02 6.50e+03 7.51e+00 bond pdb=" N GLN D 175 " pdb=" CA GLN D 175 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.32e-02 5.74e+03 6.84e+00 bond pdb=" N CYS D 261 " pdb=" CA CYS D 261 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.22e-02 6.72e+03 6.42e+00 bond pdb=" N ARG D 518 " pdb=" CA ARG D 518 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.22e+00 ... (remaining 6747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 8803 1.85 - 3.70: 315 3.70 - 5.55: 45 5.55 - 7.39: 12 7.39 - 9.24: 1 Bond angle restraints: 9176 Sorted by residual: angle pdb=" N GLU D 37 " pdb=" CA GLU D 37 " pdb=" C GLU D 37 " ideal model delta sigma weight residual 112.38 107.36 5.02 1.22e+00 6.72e-01 1.69e+01 angle pdb=" N LEU D 39 " pdb=" CA LEU D 39 " pdb=" C LEU D 39 " ideal model delta sigma weight residual 113.20 108.52 4.68 1.21e+00 6.83e-01 1.50e+01 angle pdb=" N GLN D 42 " pdb=" CA GLN D 42 " pdb=" C GLN D 42 " ideal model delta sigma weight residual 111.69 107.24 4.45 1.23e+00 6.61e-01 1.31e+01 angle pdb=" N LYS D 541 " pdb=" CA LYS D 541 " pdb=" C LYS D 541 " ideal model delta sigma weight residual 112.57 108.62 3.95 1.13e+00 7.83e-01 1.22e+01 angle pdb=" N PHE D 40 " pdb=" CA PHE D 40 " pdb=" C PHE D 40 " ideal model delta sigma weight residual 112.68 108.36 4.32 1.33e+00 5.65e-01 1.05e+01 ... (remaining 9171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3653 17.40 - 34.79: 352 34.79 - 52.19: 51 52.19 - 69.59: 18 69.59 - 86.98: 7 Dihedral angle restraints: 4081 sinusoidal: 1740 harmonic: 2341 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 28.66 64.34 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CA GLN D 139 " pdb=" C GLN D 139 " pdb=" N GLU D 140 " pdb=" CA GLU D 140 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ALA D 396 " pdb=" C ALA D 396 " pdb=" N ASN D 397 " pdb=" CA ASN D 397 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 4078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 636 0.040 - 0.080: 228 0.080 - 0.120: 92 0.120 - 0.160: 20 0.160 - 0.200: 4 Chirality restraints: 980 Sorted by residual: chirality pdb=" CG LEU A 517 " pdb=" CB LEU A 517 " pdb=" CD1 LEU A 517 " pdb=" CD2 LEU A 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA MET D 480 " pdb=" N MET D 480 " pdb=" C MET D 480 " pdb=" CB MET D 480 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 977 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 68 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C LYS D 68 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS D 68 " 0.025 2.00e-02 2.50e+03 pdb=" N TRP D 69 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 241 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C HIS D 241 " 0.051 2.00e-02 2.50e+03 pdb=" O HIS D 241 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA D 242 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 606 " -0.020 2.00e-02 2.50e+03 1.85e-02 8.53e+00 pdb=" CG TRP D 606 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 606 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 606 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 606 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 606 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 606 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 606 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 606 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 606 " 0.000 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 420 2.73 - 3.27: 6664 3.27 - 3.81: 10852 3.81 - 4.36: 13240 4.36 - 4.90: 22087 Nonbonded interactions: 53263 Sorted by model distance: nonbonded pdb=" OH TYR D 217 " pdb=" OD2 ASP D 225 " model vdw 2.185 3.040 nonbonded pdb=" NZ LYS D 475 " pdb=" OE1 GLU D 495 " model vdw 2.305 3.120 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR D 365 " pdb=" OD1 ASP D 367 " model vdw 2.334 3.040 nonbonded pdb=" NE ARG A 493 " pdb=" OE2 GLU D 35 " model vdw 2.339 3.120 ... (remaining 53258 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: 11.590 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.550 Find NCS groups from input model: 0.030 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 : 0.004 0.053 6765 Z= 0.214 Angle : 0.786 9.243 9209 Z= 0.440 Chirality : 0.049 0.200 980 Planarity : 0.008 0.072 1179 Dihedral : 13.937 86.985 2559 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.26), residues: 792 helix: -1.12 (0.22), residues: 388 sheet: 0.18 (0.63), residues: 54 loop : -1.01 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 582 TYR 0.020 0.001 TYR D 515 PHE 0.039 0.002 PHE D 274 TRP 0.050 0.003 TRP D 606 HIS 0.006 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 6752) covalent geometry : angle 0.78143 ( 9176) SS BOND : bond 0.00536 ( 6) SS BOND : angle 1.67244 ( 12) hydrogen bonds : bond 0.16018 ( 314) hydrogen bonds : angle 6.81124 ( 906) link_NAG-ASN : bond 0.00357 ( 7) link_NAG-ASN : angle 1.62063 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.193 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.4933 time to fit residues: 56.2898 Evaluate side-chains 71 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN D 42 GLN D 98 GLN D 154 ASN D 572 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.142246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.120082 restraints weight = 15416.776| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.73 r_work: 0.3873 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6765 Z= 0.197 Angle : 0.682 6.305 9209 Z= 0.355 Chirality : 0.047 0.215 980 Planarity : 0.005 0.050 1179 Dihedral : 6.444 58.761 1013 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.28 % Allowed : 10.83 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.28), residues: 792 helix: -0.02 (0.24), residues: 405 sheet: -0.24 (0.61), residues: 60 loop : -0.33 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 408 TYR 0.016 0.002 TYR D 243 PHE 0.021 0.002 PHE D 504 TRP 0.025 0.002 TRP D 606 HIS 0.006 0.002 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6752) covalent geometry : angle 0.67565 ( 9176) SS BOND : bond 0.00637 ( 6) SS BOND : angle 1.57210 ( 12) hydrogen bonds : bond 0.05445 ( 314) hydrogen bonds : angle 5.05928 ( 906) link_NAG-ASN : bond 0.00482 ( 7) link_NAG-ASN : angle 1.73991 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 219 ARG cc_start: 0.6951 (mtm-85) cc_final: 0.6634 (mtm-85) REVERT: D 482 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5944 (ttm170) outliers start: 16 outliers final: 3 residues processed: 91 average time/residue: 0.4466 time to fit residues: 43.3932 Evaluate side-chains 68 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 0.0370 chunk 53 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.142642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.120699 restraints weight = 15281.860| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.70 r_work: 0.3888 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6765 Z= 0.143 Angle : 0.628 9.323 9209 Z= 0.312 Chirality : 0.044 0.162 980 Planarity : 0.004 0.045 1179 Dihedral : 5.492 54.687 1013 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.99 % Allowed : 14.53 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.29), residues: 792 helix: 0.44 (0.25), residues: 405 sheet: -0.31 (0.61), residues: 60 loop : -0.12 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 273 TYR 0.011 0.001 TYR D 385 PHE 0.014 0.001 PHE D 369 TRP 0.023 0.002 TRP D 275 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6752) covalent geometry : angle 0.62420 ( 9176) SS BOND : bond 0.00486 ( 6) SS BOND : angle 1.13837 ( 12) hydrogen bonds : bond 0.04648 ( 314) hydrogen bonds : angle 4.80077 ( 906) link_NAG-ASN : bond 0.00377 ( 7) link_NAG-ASN : angle 1.35377 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 219 ARG cc_start: 0.6799 (mtm-85) cc_final: 0.6482 (mtm-85) outliers start: 14 outliers final: 7 residues processed: 91 average time/residue: 0.4773 time to fit residues: 46.1488 Evaluate side-chains 75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.142337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.120642 restraints weight = 15411.815| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.69 r_work: 0.3887 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6765 Z= 0.129 Angle : 0.663 18.404 9209 Z= 0.328 Chirality : 0.044 0.272 980 Planarity : 0.004 0.043 1179 Dihedral : 5.251 54.604 1013 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.56 % Allowed : 16.24 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.29), residues: 792 helix: 0.71 (0.26), residues: 405 sheet: -0.23 (0.62), residues: 59 loop : -0.06 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.017 0.001 TYR D 454 PHE 0.018 0.001 PHE D 504 TRP 0.023 0.001 TRP D 275 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6752) covalent geometry : angle 0.65547 ( 9176) SS BOND : bond 0.00844 ( 6) SS BOND : angle 2.53493 ( 12) hydrogen bonds : bond 0.04375 ( 314) hydrogen bonds : angle 4.74748 ( 906) link_NAG-ASN : bond 0.00320 ( 7) link_NAG-ASN : angle 1.23441 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 194 ASN cc_start: 0.7452 (OUTLIER) cc_final: 0.7217 (m110) REVERT: D 219 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6378 (mtm-85) outliers start: 18 outliers final: 7 residues processed: 81 average time/residue: 0.4572 time to fit residues: 39.3887 Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 591 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.140576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.119146 restraints weight = 15700.375| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.71 r_work: 0.3864 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6765 Z= 0.153 Angle : 0.663 14.080 9209 Z= 0.329 Chirality : 0.046 0.250 980 Planarity : 0.004 0.043 1179 Dihedral : 5.366 55.855 1013 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.42 % Allowed : 17.09 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.29), residues: 792 helix: 0.80 (0.26), residues: 404 sheet: -0.15 (0.63), residues: 58 loop : -0.07 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.014 0.001 TYR D 454 PHE 0.013 0.001 PHE D 369 TRP 0.022 0.002 TRP D 594 HIS 0.005 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6752) covalent geometry : angle 0.65743 ( 9176) SS BOND : bond 0.00890 ( 6) SS BOND : angle 2.03139 ( 12) hydrogen bonds : bond 0.04649 ( 314) hydrogen bonds : angle 4.73197 ( 906) link_NAG-ASN : bond 0.00363 ( 7) link_NAG-ASN : angle 1.31966 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6696 (tp) REVERT: D 290 ASN cc_start: 0.7715 (t0) cc_final: 0.7380 (t0) outliers start: 17 outliers final: 6 residues processed: 78 average time/residue: 0.4809 time to fit residues: 39.9403 Evaluate side-chains 67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.117781 restraints weight = 15363.416| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.66 r_work: 0.3844 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6765 Z= 0.168 Angle : 0.678 13.499 9209 Z= 0.337 Chirality : 0.047 0.238 980 Planarity : 0.004 0.043 1179 Dihedral : 5.528 57.454 1013 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.99 % Allowed : 17.09 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.29), residues: 792 helix: 0.77 (0.26), residues: 404 sheet: -0.15 (0.64), residues: 58 loop : -0.14 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 582 TYR 0.015 0.001 TYR D 158 PHE 0.024 0.001 PHE D 504 TRP 0.025 0.002 TRP D 275 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6752) covalent geometry : angle 0.67115 ( 9176) SS BOND : bond 0.00908 ( 6) SS BOND : angle 2.03553 ( 12) hydrogen bonds : bond 0.04857 ( 314) hydrogen bonds : angle 4.80707 ( 906) link_NAG-ASN : bond 0.00338 ( 7) link_NAG-ASN : angle 1.50281 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6882 (tp) REVERT: D 290 ASN cc_start: 0.7782 (t0) cc_final: 0.7509 (t0) outliers start: 21 outliers final: 6 residues processed: 84 average time/residue: 0.5124 time to fit residues: 45.7526 Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 62 optimal weight: 0.0570 chunk 4 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN D 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.140249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.118722 restraints weight = 15341.706| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.65 r_work: 0.3859 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6765 Z= 0.139 Angle : 0.662 12.620 9209 Z= 0.325 Chirality : 0.045 0.241 980 Planarity : 0.004 0.041 1179 Dihedral : 5.225 54.772 1013 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.99 % Allowed : 17.95 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.29), residues: 792 helix: 0.91 (0.26), residues: 401 sheet: -0.36 (0.63), residues: 58 loop : -0.09 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 219 TYR 0.014 0.001 TYR D 454 PHE 0.012 0.001 PHE D 369 TRP 0.021 0.001 TRP D 275 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6752) covalent geometry : angle 0.65798 ( 9176) SS BOND : bond 0.00924 ( 6) SS BOND : angle 1.62941 ( 12) hydrogen bonds : bond 0.04407 ( 314) hydrogen bonds : angle 4.74315 ( 906) link_NAG-ASN : bond 0.00325 ( 7) link_NAG-ASN : angle 1.30333 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6781 (mm) REVERT: D 97 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8375 (mm) REVERT: D 290 ASN cc_start: 0.7661 (t0) cc_final: 0.7386 (t0) outliers start: 21 outliers final: 8 residues processed: 89 average time/residue: 0.4642 time to fit residues: 43.8390 Evaluate side-chains 75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.139844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.118457 restraints weight = 15334.098| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.64 r_work: 0.3856 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6765 Z= 0.143 Angle : 0.679 11.891 9209 Z= 0.334 Chirality : 0.045 0.233 980 Planarity : 0.004 0.040 1179 Dihedral : 5.178 55.149 1013 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.42 % Allowed : 18.66 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.29), residues: 792 helix: 0.98 (0.26), residues: 389 sheet: -0.36 (0.64), residues: 58 loop : -0.26 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.014 0.001 TYR D 454 PHE 0.025 0.001 PHE D 504 TRP 0.018 0.001 TRP D 275 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6752) covalent geometry : angle 0.67455 ( 9176) SS BOND : bond 0.00877 ( 6) SS BOND : angle 1.62779 ( 12) hydrogen bonds : bond 0.04434 ( 314) hydrogen bonds : angle 4.76368 ( 906) link_NAG-ASN : bond 0.00307 ( 7) link_NAG-ASN : angle 1.30470 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6765 (mm) REVERT: A 364 ASP cc_start: 0.7186 (t0) cc_final: 0.6864 (t0) REVERT: D 115 ARG cc_start: 0.6246 (tpt-90) cc_final: 0.5888 (ptm-80) REVERT: D 161 ARG cc_start: 0.1851 (ttp-170) cc_final: 0.1170 (ttt180) REVERT: D 194 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7226 (m110) REVERT: D 290 ASN cc_start: 0.7675 (t0) cc_final: 0.7431 (t0) outliers start: 17 outliers final: 8 residues processed: 81 average time/residue: 0.4974 time to fit residues: 42.7893 Evaluate side-chains 74 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.139416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.118032 restraints weight = 15546.254| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.67 r_work: 0.3847 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6765 Z= 0.153 Angle : 0.694 11.933 9209 Z= 0.342 Chirality : 0.046 0.234 980 Planarity : 0.004 0.042 1179 Dihedral : 5.248 55.595 1013 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.42 % Allowed : 19.37 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.29), residues: 792 helix: 0.96 (0.26), residues: 388 sheet: -0.37 (0.65), residues: 58 loop : -0.34 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 219 TYR 0.015 0.001 TYR D 50 PHE 0.012 0.001 PHE D 369 TRP 0.018 0.001 TRP D 275 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6752) covalent geometry : angle 0.68949 ( 9176) SS BOND : bond 0.00840 ( 6) SS BOND : angle 1.68741 ( 12) hydrogen bonds : bond 0.04534 ( 314) hydrogen bonds : angle 4.79931 ( 906) link_NAG-ASN : bond 0.00309 ( 7) link_NAG-ASN : angle 1.36870 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6920 (mm) REVERT: A 364 ASP cc_start: 0.7167 (t0) cc_final: 0.6849 (t0) REVERT: D 115 ARG cc_start: 0.6204 (tpt-90) cc_final: 0.5708 (ptm-80) REVERT: D 161 ARG cc_start: 0.1997 (ttp-170) cc_final: 0.1328 (ttt180) REVERT: D 194 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7346 (m110) REVERT: D 290 ASN cc_start: 0.7703 (t0) cc_final: 0.7449 (t0) outliers start: 17 outliers final: 9 residues processed: 86 average time/residue: 0.4911 time to fit residues: 44.9233 Evaluate side-chains 78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 5.9990 chunk 40 optimal weight: 0.0770 chunk 59 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 67 optimal weight: 0.0370 chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.141463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.120423 restraints weight = 15439.101| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.68 r_work: 0.3885 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6765 Z= 0.129 Angle : 0.700 12.107 9209 Z= 0.341 Chirality : 0.045 0.223 980 Planarity : 0.004 0.042 1179 Dihedral : 4.883 53.506 1013 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.57 % Allowed : 20.23 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.29), residues: 792 helix: 1.02 (0.26), residues: 388 sheet: -0.38 (0.64), residues: 58 loop : -0.27 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 219 TYR 0.025 0.001 TYR D 237 PHE 0.029 0.001 PHE D 504 TRP 0.023 0.001 TRP D 275 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6752) covalent geometry : angle 0.69691 ( 9176) SS BOND : bond 0.00797 ( 6) SS BOND : angle 1.64341 ( 12) hydrogen bonds : bond 0.04077 ( 314) hydrogen bonds : angle 4.70939 ( 906) link_NAG-ASN : bond 0.00315 ( 7) link_NAG-ASN : angle 1.14970 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6900 (mm) REVERT: A 364 ASP cc_start: 0.7133 (t0) cc_final: 0.6854 (t0) REVERT: D 115 ARG cc_start: 0.6143 (tpt-90) cc_final: 0.5781 (ptm-80) REVERT: D 290 ASN cc_start: 0.7653 (t0) cc_final: 0.7351 (t0) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.4734 time to fit residues: 40.6013 Evaluate side-chains 75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 556 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.139811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.118865 restraints weight = 15360.336| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.65 r_work: 0.3861 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6765 Z= 0.151 Angle : 0.731 12.081 9209 Z= 0.355 Chirality : 0.048 0.425 980 Planarity : 0.004 0.043 1179 Dihedral : 5.088 55.284 1013 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.57 % Allowed : 20.94 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.29), residues: 792 helix: 0.93 (0.26), residues: 389 sheet: -0.26 (0.65), residues: 58 loop : -0.25 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 219 TYR 0.024 0.001 TYR D 237 PHE 0.036 0.001 PHE D 452 TRP 0.021 0.001 TRP D 275 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6752) covalent geometry : angle 0.72676 ( 9176) SS BOND : bond 0.00814 ( 6) SS BOND : angle 1.70362 ( 12) hydrogen bonds : bond 0.04448 ( 314) hydrogen bonds : angle 4.82355 ( 906) link_NAG-ASN : bond 0.00299 ( 7) link_NAG-ASN : angle 1.31504 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.12 seconds wall clock time: 38 minutes 4.53 seconds (2284.53 seconds total)