Starting phenix.real_space_refine on Thu Jul 2 04:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wsa_32752/07_2026/7wsa_32752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsa_32752/07_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_32752/07_2026/7wsa_32752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsa_32752/07_2026/7wsa_32752.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wsa_32752/07_2026/7wsa_32752.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wsa_32752/07_2026/7wsa_32752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wsa_32752/07_2026/7wsa_32752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsa_32752/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 chiralities: 6 Time building chain proxies: 1.35, per 1000 atoms: 0.21 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: 0.49 Conformation dependent library (CDL) restraints added in 272.0 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: 0.11 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: 0.87 Time building geometry restraints manager: 0.64 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: 3522 17.40 - 34.79: 341 34.79 - 52.19: 48 52.19 - 69.59: 16 69.59 - 86.98: 7 Dihedral angle restraints: 3934 sinusoidal: 1593 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 3931 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: 10.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.900 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 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 : 14.041 86.985 2412 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/Z covalent geometry : bond 0.00391 / 0.21 ( 6752) covalent geometry : angle 0.78143 / 0.44 ( 9176) SS BOND : bond 0.00536 / 0.27 ( 6) SS BOND : angle 1.67244 / 1.13 ( 12) hydrogen bonds : bond 0.16018 / 10.89 ( 314) hydrogen bonds : angle 6.81124 / 4.76 ( 906) link_NAG-ASN : bond 0.00357 / 0.16 ( 7) link_NAG-ASN : angle 1.62063 / 1.01 ( 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 : 0.189 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.4769 time to fit residues: 54.4978 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 : 0.175 ------------------------------------------------------------------------------- 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... 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 = 0.4280 r_free = 0.4280 target = 0.142644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.120432 restraints weight = 15421.559| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.72 r_work: 0.3876 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2435 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= 0.195 Angle : 0.676 6.127 9209 Z= 0.351 Chirality : 0.047 0.198 980 Planarity : 0.005 0.051 1179 Dihedral : 4.843 17.699 866 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.28 % Allowed : 10.97 % Favored : 86.75 % 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: -0.03 (0.24), residues: 405 sheet: -0.22 (0.61), residues: 60 loop : -0.32 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 408 TYR 0.015 0.002 TYR D 243 PHE 0.020 0.002 PHE D 504 TRP 0.025 0.002 TRP D 606 HIS 0.005 0.002 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 6752) covalent geometry : angle 0.67018 / 0.35 ( 9176) SS BOND : bond 0.00476 / 0.28 ( 6) SS BOND : angle 1.60710 / 0.87 ( 12) hydrogen bonds : bond 0.05421 / 3.57 ( 314) hydrogen bonds : angle 5.06121 / 3.64 ( 906) link_NAG-ASN : bond 0.00493 / 0.26 ( 7) link_NAG-ASN : angle 1.58752 / 0.89 ( 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 100 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 219 ARG cc_start: 0.6919 (mtm-85) cc_final: 0.6622 (mtm-85) outliers start: 16 outliers final: 3 residues processed: 90 average time/residue: 0.4021 time to fit residues: 38.7804 Evaluate side-chains 72 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL 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: 0.9980 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: 0.0670 chunk 19 optimal weight: 0.0470 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN D 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.143432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.121650 restraints weight = 15249.048| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.70 r_work: 0.3896 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6765 Z= 0.125 Angle : 0.607 9.102 9209 Z= 0.301 Chirality : 0.043 0.170 980 Planarity : 0.004 0.044 1179 Dihedral : 4.435 17.490 866 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.99 % Allowed : 13.82 % Favored : 84.19 % 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: 0.14 (0.29), residues: 792 helix: 0.50 (0.25), residues: 403 sheet: -0.41 (0.60), residues: 60 loop : -0.13 (0.33), residues: 329 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 0.012 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/Z covalent geometry : bond 0.00270 / 0.12 ( 6752) covalent geometry : angle 0.60415 / 0.30 ( 9176) SS BOND : bond 0.00383 / 0.26 ( 6) SS BOND : angle 1.14661 / 0.73 ( 12) hydrogen bonds : bond 0.04392 / 2.88 ( 314) hydrogen bonds : angle 4.74599 / 3.36 ( 906) link_NAG-ASN : bond 0.00349 / 0.16 ( 7) link_NAG-ASN : angle 1.10801 / 0.66 ( 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 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5807 (tpt) REVERT: D 161 ARG cc_start: 0.1859 (ttp-170) cc_final: 0.1130 (ttm110) outliers start: 14 outliers final: 5 residues processed: 87 average time/residue: 0.4665 time to fit residues: 43.2839 Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 152 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4274 r_free = 0.4274 target = 0.142652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.120921 restraints weight = 15300.548| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.67 r_work: 0.3892 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6765 Z= 0.133 Angle : 0.658 18.459 9209 Z= 0.324 Chirality : 0.044 0.271 980 Planarity : 0.004 0.044 1179 Dihedral : 4.400 18.878 866 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.28 % Allowed : 16.10 % Favored : 81.62 % 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: 0.79 (0.26), residues: 402 sheet: -0.30 (0.63), residues: 59 loop : 0.00 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.017 0.001 TYR D 454 PHE 0.019 0.001 PHE D 504 TRP 0.023 0.002 TRP D 275 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6752) covalent geometry : angle 0.65087 / 0.32 ( 9176) SS BOND : bond 0.00962 / 0.68 ( 6) SS BOND : angle 2.45377 / 1.29 ( 12) hydrogen bonds : bond 0.04392 / 2.88 ( 314) hydrogen bonds : angle 4.73199 / 3.36 ( 906) link_NAG-ASN : bond 0.00317 / 0.15 ( 7) link_NAG-ASN : angle 1.06887 / 0.63 ( 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: 16 poor density : 72 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 219 ARG cc_start: 0.6790 (mtm-85) cc_final: 0.6403 (mtm-85) REVERT: D 594 TRP cc_start: 0.7528 (t-100) cc_final: 0.6996 (t-100) outliers start: 16 outliers final: 8 residues processed: 81 average time/residue: 0.4125 time to fit residues: 35.7930 Evaluate side-chains 74 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 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 91 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN 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 = 0.139903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.118463 restraints weight = 15534.463| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.70 r_work: 0.3855 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6765 Z= 0.167 Angle : 0.683 14.193 9209 Z= 0.340 Chirality : 0.046 0.250 980 Planarity : 0.004 0.044 1179 Dihedral : 4.654 19.008 866 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.28 % Allowed : 17.09 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.75 (0.26), residues: 404 sheet: -0.27 (0.63), residues: 58 loop : -0.11 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.019 0.002 TYR D 279 PHE 0.013 0.001 PHE D 369 TRP 0.022 0.001 TRP D 275 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 6752) covalent geometry : angle 0.67715 / 0.34 ( 9176) SS BOND : bond 0.00852 / 0.60 ( 6) SS BOND : angle 2.04331 / 1.20 ( 12) hydrogen bonds : bond 0.04860 / 3.14 ( 314) hydrogen bonds : angle 4.82225 / 3.44 ( 906) link_NAG-ASN : bond 0.00359 / 0.17 ( 7) link_NAG-ASN : angle 1.27319 / 0.76 ( 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 90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6698 (tp) REVERT: D 290 ASN cc_start: 0.7729 (t0) cc_final: 0.7432 (t0) outliers start: 16 outliers final: 6 residues processed: 84 average time/residue: 0.4331 time to fit residues: 38.8904 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 : 0.191 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.139341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.117949 restraints weight = 15361.944| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.65 r_work: 0.3849 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4070 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= 0.166 Angle : 0.687 13.484 9209 Z= 0.340 Chirality : 0.046 0.235 980 Planarity : 0.004 0.044 1179 Dihedral : 4.620 19.424 866 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.99 % Allowed : 17.81 % Favored : 79.20 % 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: 0.44 (0.29), residues: 792 helix: 0.81 (0.26), residues: 401 sheet: -0.25 (0.64), residues: 58 loop : -0.10 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.014 0.001 TYR D 454 PHE 0.019 0.001 PHE D 504 TRP 0.026 0.002 TRP D 275 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 6752) covalent geometry : angle 0.68143 / 0.34 ( 9176) SS BOND : bond 0.00887 / 0.63 ( 6) SS BOND : angle 1.95146 / 1.36 ( 12) hydrogen bonds : bond 0.04771 / 3.10 ( 314) hydrogen bonds : angle 4.79528 / 3.40 ( 906) link_NAG-ASN : bond 0.00342 / 0.19 ( 7) link_NAG-ASN : angle 1.39921 / 0.85 ( 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 88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6850 (tp) REVERT: D 97 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8375 (mm) REVERT: D 98 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7879 (mm110) REVERT: D 290 ASN cc_start: 0.7750 (t0) cc_final: 0.7452 (t0) outliers start: 21 outliers final: 8 residues processed: 81 average time/residue: 0.4232 time to fit residues: 36.6002 Evaluate side-chains 75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain D residue 98 GLN 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 Chi-restraints excluded: chain D residue 580 ASN 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: 1.9990 chunk 44 optimal weight: 0.0170 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 62 optimal weight: 0.0470 chunk 4 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4237 r_free = 0.4237 target = 0.139904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.118455 restraints weight = 15296.901| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.66 r_work: 0.3856 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6765 Z= 0.146 Angle : 0.678 12.795 9209 Z= 0.333 Chirality : 0.045 0.241 980 Planarity : 0.004 0.042 1179 Dihedral : 4.526 18.946 866 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.42 % Allowed : 17.52 % 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: 0.40 (0.29), residues: 792 helix: 0.82 (0.26), residues: 401 sheet: -0.46 (0.63), residues: 58 loop : -0.13 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 219 TYR 0.015 0.001 TYR D 454 PHE 0.012 0.001 PHE D 369 TRP 0.022 0.001 TRP D 275 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6752) covalent geometry : angle 0.67428 / 0.33 ( 9176) SS BOND : bond 0.01090 / 0.78 ( 6) SS BOND : angle 1.64781 / 0.88 ( 12) hydrogen bonds : bond 0.04512 / 2.94 ( 314) hydrogen bonds : angle 4.75886 / 3.37 ( 906) link_NAG-ASN : bond 0.00297 / 0.15 ( 7) link_NAG-ASN : angle 1.24259 / 0.76 ( 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 99 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 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: 0.7090 (OUTLIER) cc_final: 0.6764 (mm) REVERT: D 161 ARG cc_start: 0.2230 (ttp-170) cc_final: 0.1367 (ttp-170) REVERT: D 194 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7242 (m110) REVERT: D 290 ASN cc_start: 0.7686 (t0) cc_final: 0.7425 (t0) REVERT: D 598 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6330 (tp-100) outliers start: 24 outliers final: 11 residues processed: 91 average time/residue: 0.4505 time to fit residues: 43.7294 Evaluate side-chains 83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 485 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 Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 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: 0.6980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.139300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.117845 restraints weight = 15275.688| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.67 r_work: 0.3847 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6765 Z= 0.156 Angle : 0.700 12.165 9209 Z= 0.342 Chirality : 0.046 0.238 980 Planarity : 0.004 0.041 1179 Dihedral : 4.531 18.723 866 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.13 % Allowed : 18.52 % Favored : 78.35 % 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: 0.92 (0.26), residues: 395 sheet: -0.47 (0.64), residues: 58 loop : -0.21 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.016 0.001 TYR D 454 PHE 0.020 0.001 PHE D 504 TRP 0.020 0.001 TRP D 275 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 6752) covalent geometry : angle 0.69578 / 0.34 ( 9176) SS BOND : bond 0.00978 / 0.69 ( 6) SS BOND : angle 1.65410 / 0.96 ( 12) hydrogen bonds : bond 0.04618 / 2.98 ( 314) hydrogen bonds : angle 4.79416 / 3.42 ( 906) link_NAG-ASN : bond 0.00288 / 0.15 ( 7) link_NAG-ASN : angle 1.34944 / 0.83 ( 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 95 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6841 (mm) REVERT: A 364 ASP cc_start: 0.7190 (t0) cc_final: 0.6886 (t0) REVERT: D 97 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8382 (mm) REVERT: D 115 ARG cc_start: 0.6155 (tpt-90) cc_final: 0.5859 (ptm-80) REVERT: D 194 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7211 (m110) REVERT: D 598 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.6276 (tp-100) outliers start: 22 outliers final: 11 residues processed: 89 average time/residue: 0.4249 time to fit residues: 40.3504 Evaluate side-chains 79 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 97 LEU 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 485 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 Chi-restraints excluded: chain D residue 598 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.138758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.117382 restraints weight = 15450.478| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.67 r_work: 0.3837 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6765 Z= 0.168 Angle : 0.718 11.947 9209 Z= 0.352 Chirality : 0.047 0.234 980 Planarity : 0.004 0.042 1179 Dihedral : 4.636 18.792 866 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.71 % Allowed : 19.09 % 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: 0.39 (0.29), residues: 792 helix: 0.90 (0.26), residues: 395 sheet: -0.45 (0.64), residues: 58 loop : -0.24 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 219 TYR 0.018 0.002 TYR D 515 PHE 0.030 0.001 PHE D 452 TRP 0.018 0.001 TRP D 275 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 6752) covalent geometry : angle 0.71317 / 0.35 ( 9176) SS BOND : bond 0.00932 / 0.66 ( 6) SS BOND : angle 1.68589 / 1.04 ( 12) hydrogen bonds : bond 0.04717 / 3.05 ( 314) hydrogen bonds : angle 4.80654 / 3.41 ( 906) link_NAG-ASN : bond 0.00286 / 0.15 ( 7) link_NAG-ASN : angle 1.38783 / 0.86 ( 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 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6861 (mm) REVERT: A 364 ASP cc_start: 0.7199 (t0) cc_final: 0.6900 (t0) REVERT: D 161 ARG cc_start: 0.1898 (ttp-170) cc_final: 0.1145 (ttp-170) REVERT: D 598 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.6180 (tp-100) outliers start: 19 outliers final: 11 residues processed: 87 average time/residue: 0.4058 time to fit residues: 37.5764 Evaluate side-chains 78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 433 VAL 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 364 VAL Chi-restraints excluded: chain D residue 485 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 Chi-restraints excluded: chain D residue 598 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.0570 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.138463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.116497 restraints weight = 15231.880| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.68 r_work: 0.3785 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6765 Z= 0.145 Angle : 0.710 11.609 9209 Z= 0.344 Chirality : 0.046 0.228 980 Planarity : 0.004 0.042 1179 Dihedral : 4.519 18.348 866 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.99 % Allowed : 20.66 % Favored : 77.35 % 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: 0.41 (0.30), residues: 792 helix: 0.95 (0.26), residues: 389 sheet: -0.50 (0.64), residues: 58 loop : -0.26 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 273 TYR 0.019 0.001 TYR D 454 PHE 0.031 0.001 PHE D 452 TRP 0.026 0.001 TRP D 275 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6752) covalent geometry : angle 0.70663 / 0.34 ( 9176) SS BOND : bond 0.00839 / 0.59 ( 6) SS BOND : angle 1.64893 / 1.06 ( 12) hydrogen bonds : bond 0.04426 / 2.88 ( 314) hydrogen bonds : angle 4.74095 / 3.36 ( 906) link_NAG-ASN : bond 0.00296 / 0.14 ( 7) link_NAG-ASN : angle 1.21843 / 0.78 ( 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 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6942 (mm) REVERT: A 364 ASP cc_start: 0.7195 (t0) cc_final: 0.6902 (t0) REVERT: D 115 ARG cc_start: 0.6213 (tpt-90) cc_final: 0.5756 (ptm-80) REVERT: D 161 ARG cc_start: 0.2062 (ttp-170) cc_final: 0.1327 (ttp-170) REVERT: D 504 PHE cc_start: 0.6966 (t80) cc_final: 0.6763 (t80) REVERT: D 598 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.6269 (tp-100) outliers start: 14 outliers final: 11 residues processed: 82 average time/residue: 0.4090 time to fit residues: 35.8174 Evaluate side-chains 77 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL 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 364 VAL Chi-restraints excluded: chain D residue 485 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 Chi-restraints excluded: chain D residue 598 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 59 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 0.0010 chunk 34 optimal weight: 4.9990 overall best weight: 0.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN D 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.141363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.120286 restraints weight = 15281.332| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.68 r_work: 0.3881 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6765 Z= 0.132 Angle : 0.717 11.661 9209 Z= 0.347 Chirality : 0.045 0.219 980 Planarity : 0.004 0.041 1179 Dihedral : 4.409 18.581 866 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.99 % Allowed : 20.66 % Favored : 77.35 % 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 (0.30), residues: 792 helix: 1.00 (0.26), residues: 388 sheet: -0.27 (0.66), residues: 53 loop : -0.25 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 219 TYR 0.033 0.001 TYR A 380 PHE 0.023 0.001 PHE D 452 TRP 0.023 0.001 TRP D 275 HIS 0.004 0.001 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6752) covalent geometry : angle 0.71317 / 0.35 ( 9176) SS BOND : bond 0.00562 / 0.40 ( 6) SS BOND : angle 1.92903 / 1.16 ( 12) hydrogen bonds : bond 0.04096 / 2.68 ( 314) hydrogen bonds : angle 4.63879 / 3.30 ( 906) link_NAG-ASN : bond 0.00290 / 0.14 ( 7) link_NAG-ASN : angle 1.05183 / 0.69 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.49 seconds wall clock time: 36 minutes 58.65 seconds (2218.65 seconds total)