Starting phenix.real_space_refine on Thu Jul 2 04:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dm6_27528/07_2026/8dm6_27528.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm6_27528/07_2026/8dm6_27528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2026/8dm6_27528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2026/8dm6_27528.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2026/8dm6_27528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2026/8dm6_27528.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2026/8dm6_27528.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2026/8dm6_27528.cif" } resolution = 2.77 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= -0.001 sd= 0.016 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 4200 2.51 5 N 1082 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 6559 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1604 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: 1.45, per 1000 atoms: 0.22 Number of scatterers: 6559 At special positions: 0 Unit cell: (79, 86, 122, 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 1240 8.00 N 1082 7.00 C 4200 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.02 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: 0.55 Conformation dependent library (CDL) restraints added in 346.5 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: 1500 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 57.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.866A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.572A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.284A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 20 through 53 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: 4.166A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.620A 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: 3.609A 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: 3.807A 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: 4.500A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.824A 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 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.744A 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 397 through 413 removed outlier: 4.340A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.531A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.335A 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: 3.747A 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: 4.372A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.992A 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: 6.539A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.976A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.246A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 984 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: 0.99 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2084 1.35 - 1.48: 1851 1.48 - 1.61: 2752 1.61 - 1.73: 0 1.73 - 1.86: 58 Bond restraints: 6745 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C1 NAG D 706 " pdb=" O5 NAG D 706 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.575 -0.072 3.40e-02 8.65e+02 4.47e+00 bond pdb=" C1 NAG D 704 " pdb=" O5 NAG D 704 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.52e+00 ... (remaining 6740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 8890 2.44 - 4.87: 244 4.87 - 7.31: 21 7.31 - 9.74: 7 9.74 - 12.18: 4 Bond angle restraints: 9166 Sorted by residual: angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 120.82 -11.01 2.21e+00 2.05e-01 2.48e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 125.13 -10.73 2.30e+00 1.89e-01 2.18e+01 angle pdb=" CB MET D 152 " pdb=" CG MET D 152 " pdb=" SD MET D 152 " ideal model delta sigma weight residual 112.70 124.88 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB LYS D 534 " pdb=" CG LYS D 534 " pdb=" CD LYS D 534 " ideal model delta sigma weight residual 111.30 120.35 -9.05 2.30e+00 1.89e-01 1.55e+01 angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 ... (remaining 9161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 3519 17.48 - 34.97: 333 34.97 - 52.45: 50 52.45 - 69.94: 13 69.94 - 87.42: 8 Dihedral angle restraints: 3923 sinusoidal: 1586 harmonic: 2337 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 38.29 54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 55.17 37.83 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 588 0.046 - 0.093: 273 0.093 - 0.139: 86 0.139 - 0.185: 24 0.185 - 0.231: 5 Chirality restraints: 976 Sorted by residual: chirality pdb=" CA ASN A 360 " pdb=" N ASN A 360 " pdb=" C ASN A 360 " pdb=" CB ASN A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU D 267 " pdb=" CB LEU D 267 " pdb=" CD1 LEU D 267 " pdb=" CD2 LEU D 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB THR A 333 " pdb=" CA THR A 333 " pdb=" OG1 THR A 333 " pdb=" CG2 THR A 333 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 973 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS D 241 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C HIS D 241 " 0.054 2.00e-02 2.50e+03 pdb=" O HIS D 241 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA D 242 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 244 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C VAL D 244 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL D 244 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG D 245 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 226 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C VAL D 226 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL D 226 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU D 227 " -0.017 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1832 2.81 - 3.33: 5953 3.33 - 3.85: 11478 3.85 - 4.38: 13089 4.38 - 4.90: 22516 Nonbonded interactions: 54868 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.342 3.040 nonbonded pdb=" OE2 GLU D 435 " pdb=" NZ LYS D 541 " model vdw 2.343 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.360 3.040 ... (remaining 54863 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: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.020 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:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.006 0.072 6758 Z= 0.276 Angle : 0.948 12.179 9199 Z= 0.513 Chirality : 0.059 0.231 976 Planarity : 0.007 0.063 1179 Dihedral : 14.085 87.420 2405 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.57 % Allowed : 4.29 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.27), residues: 792 helix: 0.27 (0.23), residues: 389 sheet: 2.01 (0.81), residues: 34 loop : -0.50 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 457 TYR 0.031 0.002 TYR D 385 PHE 0.024 0.003 PHE A 377 TRP 0.019 0.002 TRP D 594 HIS 0.007 0.002 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.28 ( 6745) covalent geometry : angle 0.93686 / 0.51 ( 9166) SS BOND : bond 0.00805 / 0.46 ( 6) SS BOND : angle 2.14270 / 1.35 ( 12) hydrogen bonds : bond 0.14801 / 10.23 ( 321) hydrogen bonds : angle 6.64435 / 4.64 ( 984) link_NAG-ASN : bond 0.00496 / 0.22 ( 7) link_NAG-ASN : angle 2.86529 / 2.25 ( 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 194 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7820 (ttt90) REVERT: A 465 GLU cc_start: 0.8263 (tt0) cc_final: 0.8028 (tt0) REVERT: D 55 THR cc_start: 0.8054 (m) cc_final: 0.7795 (p) REVERT: D 270 MET cc_start: 0.8145 (tpt) cc_final: 0.7927 (tpp) REVERT: D 366 MET cc_start: 0.8582 (ttp) cc_final: 0.8363 (ttp) REVERT: D 483 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8173 (tm-30) REVERT: D 534 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8302 (mmtm) REVERT: D 582 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7744 (mmm160) REVERT: D 603 PHE cc_start: 0.8656 (t80) cc_final: 0.8027 (t80) REVERT: D 604 VAL cc_start: 0.9243 (p) cc_final: 0.8911 (t) outliers start: 4 outliers final: 1 residues processed: 192 average time/residue: 0.6204 time to fit residues: 124.4190 Evaluate side-chains 119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN D 42 GLN D 76 GLN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079964 restraints weight = 12246.295| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.83 r_work: 0.2974 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6758 Z= 0.164 Angle : 0.619 7.299 9199 Z= 0.317 Chirality : 0.044 0.186 976 Planarity : 0.005 0.036 1179 Dihedral : 4.378 23.473 867 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.72 % Allowed : 14.16 % Favored : 83.12 % 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: 0.73 (0.28), residues: 792 helix: 1.01 (0.25), residues: 401 sheet: 1.22 (0.74), residues: 43 loop : -0.12 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 582 TYR 0.016 0.001 TYR D 41 PHE 0.014 0.001 PHE D 369 TRP 0.017 0.001 TRP D 165 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 6745) covalent geometry : angle 0.60606 / 0.31 ( 9166) SS BOND : bond 0.00513 / 0.31 ( 6) SS BOND : angle 1.31946 / 0.81 ( 12) hydrogen bonds : bond 0.05175 / 3.45 ( 321) hydrogen bonds : angle 5.06137 / 3.54 ( 984) link_NAG-ASN : bond 0.00406 / 0.20 ( 7) link_NAG-ASN : angle 2.57962 / 1.65 ( 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 135 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8136 (p0) cc_final: 0.7825 (p0) REVERT: A 340 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8675 (mp0) REVERT: A 357 ARG cc_start: 0.8759 (ptm160) cc_final: 0.8208 (ttt90) REVERT: A 465 GLU cc_start: 0.8605 (tt0) cc_final: 0.8229 (tt0) REVERT: D 23 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8492 (pt0) REVERT: D 26 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8351 (mtmm) REVERT: D 55 THR cc_start: 0.7941 (m) cc_final: 0.7565 (p) REVERT: D 182 GLU cc_start: 0.8556 (tt0) cc_final: 0.8139 (tt0) REVERT: D 228 HIS cc_start: 0.8443 (t70) cc_final: 0.7974 (m90) REVERT: D 270 MET cc_start: 0.8240 (tpt) cc_final: 0.7931 (tpp) REVERT: D 287 GLN cc_start: 0.8665 (mp10) cc_final: 0.8242 (pm20) REVERT: D 408 MET cc_start: 0.9239 (mmt) cc_final: 0.8967 (mmt) REVERT: D 429 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8159 (mm-40) REVERT: D 467 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7721 (mp0) REVERT: D 472 GLN cc_start: 0.8263 (mm-40) cc_final: 0.8055 (mm-40) REVERT: D 483 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8250 (tm-30) REVERT: D 497 TYR cc_start: 0.8783 (m-80) cc_final: 0.8561 (m-80) REVERT: D 603 PHE cc_start: 0.8730 (t80) cc_final: 0.8319 (t80) outliers start: 19 outliers final: 4 residues processed: 127 average time/residue: 0.6204 time to fit residues: 82.4290 Evaluate side-chains 109 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain D residue 429 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 32 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.0060 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.079314 restraints weight = 12182.669| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.77 r_work: 0.2945 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6758 Z= 0.149 Angle : 0.577 8.679 9199 Z= 0.290 Chirality : 0.042 0.293 976 Planarity : 0.004 0.034 1179 Dihedral : 4.144 19.878 865 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.15 % Allowed : 15.02 % Favored : 81.83 % 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: 1.08 (0.29), residues: 792 helix: 1.30 (0.25), residues: 402 sheet: 2.04 (0.87), residues: 33 loop : -0.01 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.015 0.001 TYR D 50 PHE 0.014 0.001 PHE D 369 TRP 0.013 0.001 TRP D 165 HIS 0.002 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 6745) covalent geometry : angle 0.56247 / 0.29 ( 9166) SS BOND : bond 0.00479 / 0.28 ( 6) SS BOND : angle 1.13540 / 0.70 ( 12) hydrogen bonds : bond 0.04829 / 3.21 ( 321) hydrogen bonds : angle 4.78062 / 3.34 ( 984) link_NAG-ASN : bond 0.00287 / 0.14 ( 7) link_NAG-ASN : angle 2.63094 / 1.59 ( 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 134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8322 (p0) cc_final: 0.7706 (p0) REVERT: A 340 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8688 (mp0) REVERT: A 346 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7287 (ppp-140) REVERT: A 357 ARG cc_start: 0.8736 (ptm160) cc_final: 0.8052 (ttt90) REVERT: A 405 ASN cc_start: 0.8838 (m-40) cc_final: 0.8608 (m110) REVERT: A 465 GLU cc_start: 0.8642 (tt0) cc_final: 0.8337 (tt0) REVERT: D 26 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8365 (mtmm) REVERT: D 55 THR cc_start: 0.8049 (m) cc_final: 0.7684 (p) REVERT: D 115 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8002 (tpm170) REVERT: D 182 GLU cc_start: 0.8643 (tt0) cc_final: 0.8278 (tt0) REVERT: D 228 HIS cc_start: 0.8461 (t70) cc_final: 0.7968 (m90) REVERT: D 270 MET cc_start: 0.8201 (tpt) cc_final: 0.7910 (tpp) REVERT: D 287 GLN cc_start: 0.8667 (mp10) cc_final: 0.8142 (pm20) REVERT: D 305 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: D 472 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8056 (mm-40) REVERT: D 483 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8260 (tm-30) REVERT: D 497 TYR cc_start: 0.8850 (m-80) cc_final: 0.8643 (m-80) REVERT: D 603 PHE cc_start: 0.8789 (t80) cc_final: 0.8336 (t80) outliers start: 22 outliers final: 9 residues processed: 123 average time/residue: 0.6137 time to fit residues: 79.2573 Evaluate side-chains 117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 549 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 0.0050 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078204 restraints weight = 12320.644| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.88 r_work: 0.2935 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6758 Z= 0.151 Angle : 0.563 6.515 9199 Z= 0.282 Chirality : 0.042 0.194 976 Planarity : 0.004 0.031 1179 Dihedral : 4.026 16.477 865 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.00 % Allowed : 17.17 % Favored : 79.83 % 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: 1.25 (0.29), residues: 792 helix: 1.38 (0.25), residues: 408 sheet: 1.89 (0.87), residues: 33 loop : 0.18 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 306 TYR 0.014 0.001 TYR D 50 PHE 0.014 0.001 PHE D 369 TRP 0.012 0.001 TRP D 165 HIS 0.003 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6745) covalent geometry : angle 0.55684 / 0.28 ( 9166) SS BOND : bond 0.00465 / 0.27 ( 6) SS BOND : angle 1.10953 / 0.67 ( 12) hydrogen bonds : bond 0.04728 / 3.13 ( 321) hydrogen bonds : angle 4.64832 / 3.25 ( 984) link_NAG-ASN : bond 0.00207 / 0.09 ( 7) link_NAG-ASN : angle 1.67184 / 1.18 ( 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 130 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8452 (p0) cc_final: 0.8009 (p0) REVERT: A 340 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8688 (mp0) REVERT: A 357 ARG cc_start: 0.8725 (ptm160) cc_final: 0.8128 (ttt90) REVERT: A 405 ASN cc_start: 0.8821 (m-40) cc_final: 0.8603 (m110) REVERT: A 465 GLU cc_start: 0.8663 (tt0) cc_final: 0.8312 (tt0) REVERT: D 23 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8564 (pt0) REVERT: D 26 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8298 (mttm) REVERT: D 55 THR cc_start: 0.8104 (m) cc_final: 0.7770 (p) REVERT: D 115 ARG cc_start: 0.8572 (tpm-80) cc_final: 0.7854 (tpm170) REVERT: D 182 GLU cc_start: 0.8655 (tt0) cc_final: 0.8329 (tt0) REVERT: D 270 MET cc_start: 0.8110 (tpt) cc_final: 0.7841 (tpp) REVERT: D 287 GLN cc_start: 0.8661 (mp10) cc_final: 0.8165 (pm20) REVERT: D 435 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8538 (mm-30) REVERT: D 467 GLU cc_start: 0.8282 (mp0) cc_final: 0.7585 (mp0) REVERT: D 472 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8122 (mm-40) REVERT: D 479 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8470 (mt-10) REVERT: D 483 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 531 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8348 (mt0) REVERT: D 582 ARG cc_start: 0.8393 (mmm-85) cc_final: 0.7739 (mmm160) REVERT: D 603 PHE cc_start: 0.8793 (t80) cc_final: 0.8337 (t80) outliers start: 21 outliers final: 9 residues processed: 121 average time/residue: 0.6365 time to fit residues: 80.6346 Evaluate side-chains 114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.100068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.077137 restraints weight = 12318.590| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.85 r_work: 0.2914 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6758 Z= 0.174 Angle : 0.572 6.848 9199 Z= 0.287 Chirality : 0.042 0.155 976 Planarity : 0.004 0.031 1179 Dihedral : 4.041 16.380 865 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.72 % Allowed : 17.88 % Favored : 79.40 % 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: 1.32 (0.29), residues: 792 helix: 1.45 (0.26), residues: 409 sheet: 0.75 (0.75), residues: 43 loop : 0.33 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.013 0.001 TYR D 50 PHE 0.014 0.001 PHE D 369 TRP 0.011 0.001 TRP D 165 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 6745) covalent geometry : angle 0.56642 / 0.29 ( 9166) SS BOND : bond 0.00586 / 0.39 ( 6) SS BOND : angle 1.22585 / 0.71 ( 12) hydrogen bonds : bond 0.04821 / 3.20 ( 321) hydrogen bonds : angle 4.61977 / 3.23 ( 984) link_NAG-ASN : bond 0.00191 / 0.09 ( 7) link_NAG-ASN : angle 1.52968 / 1.13 ( 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 126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.8653 (tt0) cc_final: 0.8314 (tt0) REVERT: D 26 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8386 (mttp) REVERT: D 55 THR cc_start: 0.8188 (m) cc_final: 0.7881 (p) REVERT: D 115 ARG cc_start: 0.8701 (tpm-80) cc_final: 0.8258 (tpm170) REVERT: D 182 GLU cc_start: 0.8707 (tt0) cc_final: 0.8371 (tt0) REVERT: D 270 MET cc_start: 0.8198 (tpt) cc_final: 0.7980 (tpp) REVERT: D 287 GLN cc_start: 0.8671 (mp10) cc_final: 0.8198 (pm20) REVERT: D 467 GLU cc_start: 0.8326 (mp0) cc_final: 0.7276 (mp0) REVERT: D 472 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8150 (mm-40) REVERT: D 479 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8477 (mt-10) REVERT: D 483 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8326 (tm-30) REVERT: D 531 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8295 (mt0) REVERT: D 582 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.7795 (mmm160) REVERT: D 603 PHE cc_start: 0.8845 (t80) cc_final: 0.8415 (t80) outliers start: 19 outliers final: 10 residues processed: 118 average time/residue: 0.5844 time to fit residues: 72.4837 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078131 restraints weight = 12181.898| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.83 r_work: 0.2917 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6758 Z= 0.146 Angle : 0.557 7.306 9199 Z= 0.278 Chirality : 0.041 0.152 976 Planarity : 0.003 0.031 1179 Dihedral : 3.953 16.421 865 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.43 % Allowed : 19.17 % Favored : 78.40 % 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: 1.36 (0.29), residues: 792 helix: 1.57 (0.26), residues: 403 sheet: 0.74 (0.75), residues: 43 loop : 0.25 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.013 0.001 TYR D 41 PHE 0.014 0.001 PHE D 369 TRP 0.011 0.001 TRP D 165 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 6745) covalent geometry : angle 0.55233 / 0.28 ( 9166) SS BOND : bond 0.00563 / 0.36 ( 6) SS BOND : angle 1.13885 / 0.68 ( 12) hydrogen bonds : bond 0.04595 / 3.05 ( 321) hydrogen bonds : angle 4.56222 / 3.19 ( 984) link_NAG-ASN : bond 0.00205 / 0.08 ( 7) link_NAG-ASN : angle 1.43808 / 1.07 ( 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 125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8710 (mp0) REVERT: A 357 ARG cc_start: 0.8679 (ptm160) cc_final: 0.8155 (ttt90) REVERT: A 465 GLU cc_start: 0.8642 (tt0) cc_final: 0.8312 (tt0) REVERT: D 26 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8346 (mttm) REVERT: D 55 THR cc_start: 0.8164 (m) cc_final: 0.7800 (p) REVERT: D 114 LYS cc_start: 0.9450 (pptt) cc_final: 0.9232 (tmmt) REVERT: D 115 ARG cc_start: 0.8679 (tpm-80) cc_final: 0.8295 (tpm170) REVERT: D 213 ASP cc_start: 0.9072 (t70) cc_final: 0.8712 (t0) REVERT: D 270 MET cc_start: 0.8299 (tpt) cc_final: 0.8033 (tpp) REVERT: D 287 GLN cc_start: 0.8682 (mp10) cc_final: 0.8214 (pm20) REVERT: D 383 MET cc_start: 0.8880 (mtm) cc_final: 0.8664 (mtp) REVERT: D 467 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: D 471 ASP cc_start: 0.8920 (p0) cc_final: 0.8152 (p0) REVERT: D 472 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7972 (mm-40) REVERT: D 479 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8397 (mt-10) REVERT: D 483 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8318 (tm-30) REVERT: D 497 TYR cc_start: 0.8727 (m-80) cc_final: 0.8286 (m-80) REVERT: D 531 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: D 603 PHE cc_start: 0.8831 (t80) cc_final: 0.8406 (t80) outliers start: 17 outliers final: 8 residues processed: 118 average time/residue: 0.5939 time to fit residues: 73.7177 Evaluate side-chains 115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077834 restraints weight = 12015.455| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.80 r_work: 0.2911 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6758 Z= 0.150 Angle : 0.564 7.867 9199 Z= 0.282 Chirality : 0.042 0.154 976 Planarity : 0.003 0.029 1179 Dihedral : 3.933 16.430 865 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.29 % Allowed : 19.89 % Favored : 77.83 % 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: 1.39 (0.29), residues: 792 helix: 1.60 (0.26), residues: 403 sheet: 0.72 (0.75), residues: 43 loop : 0.25 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.013 0.001 TYR D 41 PHE 0.014 0.001 PHE D 369 TRP 0.013 0.001 TRP D 478 HIS 0.003 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 6745) covalent geometry : angle 0.55971 / 0.28 ( 9166) SS BOND : bond 0.00533 / 0.34 ( 6) SS BOND : angle 1.10589 / 0.66 ( 12) hydrogen bonds : bond 0.04594 / 3.05 ( 321) hydrogen bonds : angle 4.54512 / 3.17 ( 984) link_NAG-ASN : bond 0.00184 / 0.07 ( 7) link_NAG-ASN : angle 1.41282 / 1.06 ( 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 118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.8643 (tt0) cc_final: 0.8322 (tt0) REVERT: D 26 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8328 (mttm) REVERT: D 213 ASP cc_start: 0.9066 (t70) cc_final: 0.8713 (t0) REVERT: D 270 MET cc_start: 0.8191 (tpt) cc_final: 0.7989 (tpp) REVERT: D 287 GLN cc_start: 0.8711 (mp10) cc_final: 0.8236 (pm20) REVERT: D 467 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: D 479 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8394 (mt-10) REVERT: D 483 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8317 (tm-30) REVERT: D 497 TYR cc_start: 0.8742 (m-80) cc_final: 0.8355 (m-80) REVERT: D 531 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: D 582 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8099 (mmm160) REVERT: D 603 PHE cc_start: 0.8826 (t80) cc_final: 0.8404 (t80) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.6232 time to fit residues: 71.9636 Evaluate side-chains 111 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.099614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076745 restraints weight = 12163.625| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.82 r_work: 0.2894 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6758 Z= 0.171 Angle : 0.574 8.228 9199 Z= 0.288 Chirality : 0.042 0.158 976 Planarity : 0.003 0.029 1179 Dihedral : 3.987 16.352 865 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.58 % Allowed : 20.31 % Favored : 77.11 % 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: 1.32 (0.29), residues: 792 helix: 1.46 (0.25), residues: 410 sheet: 0.69 (0.75), residues: 43 loop : 0.32 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.013 0.001 TYR D 41 PHE 0.015 0.001 PHE D 369 TRP 0.017 0.001 TRP D 478 HIS 0.003 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 6745) covalent geometry : angle 0.56964 / 0.29 ( 9166) SS BOND : bond 0.00538 / 0.34 ( 6) SS BOND : angle 1.04435 / 0.61 ( 12) hydrogen bonds : bond 0.04732 / 3.14 ( 321) hydrogen bonds : angle 4.57220 / 3.19 ( 984) link_NAG-ASN : bond 0.00205 / 0.09 ( 7) link_NAG-ASN : angle 1.45316 / 1.11 ( 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 118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.8645 (tt0) cc_final: 0.8321 (tt0) REVERT: D 26 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8327 (mttm) REVERT: D 114 LYS cc_start: 0.9462 (pptt) cc_final: 0.9240 (ttpp) REVERT: D 115 ARG cc_start: 0.8743 (tpm-80) cc_final: 0.8507 (tpm170) REVERT: D 213 ASP cc_start: 0.9068 (t70) cc_final: 0.8717 (t0) REVERT: D 243 TYR cc_start: 0.8974 (t80) cc_final: 0.8741 (t80) REVERT: D 287 GLN cc_start: 0.8690 (mp10) cc_final: 0.8244 (pm20) REVERT: D 305 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: D 467 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: D 471 ASP cc_start: 0.8929 (p0) cc_final: 0.8112 (p0) REVERT: D 472 GLN cc_start: 0.8628 (mt0) cc_final: 0.8170 (mm-40) REVERT: D 479 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8436 (mt-10) REVERT: D 483 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8338 (tm-30) REVERT: D 497 TYR cc_start: 0.8754 (m-80) cc_final: 0.8358 (m-80) REVERT: D 531 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: D 582 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8090 (mmm160) REVERT: D 603 PHE cc_start: 0.8821 (t80) cc_final: 0.8396 (t80) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.4698 time to fit residues: 54.1999 Evaluate side-chains 112 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.099921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076929 restraints weight = 12287.576| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.86 r_work: 0.2915 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6758 Z= 0.147 Angle : 0.578 8.647 9199 Z= 0.289 Chirality : 0.042 0.160 976 Planarity : 0.003 0.029 1179 Dihedral : 3.968 16.290 865 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.58 % Allowed : 19.89 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.32 (0.29), residues: 792 helix: 1.56 (0.26), residues: 403 sheet: 0.66 (0.75), residues: 43 loop : 0.19 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.012 0.001 TYR D 41 PHE 0.014 0.001 PHE D 369 TRP 0.017 0.001 TRP D 478 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6745) covalent geometry : angle 0.57377 / 0.29 ( 9166) SS BOND : bond 0.00514 / 0.32 ( 6) SS BOND : angle 1.15576 / 0.69 ( 12) hydrogen bonds : bond 0.04574 / 3.02 ( 321) hydrogen bonds : angle 4.54415 / 3.18 ( 984) link_NAG-ASN : bond 0.00203 / 0.08 ( 7) link_NAG-ASN : angle 1.42583 / 1.08 ( 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 120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.8629 (tt0) cc_final: 0.8303 (tt0) REVERT: D 26 LYS cc_start: 0.8562 (mtpt) cc_final: 0.8209 (mttm) REVERT: D 197 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8082 (mp0) REVERT: D 213 ASP cc_start: 0.9081 (t70) cc_final: 0.8731 (t0) REVERT: D 243 TYR cc_start: 0.8822 (t80) cc_final: 0.8585 (t80) REVERT: D 287 GLN cc_start: 0.8700 (mp10) cc_final: 0.8270 (pm20) REVERT: D 305 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: D 467 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: D 471 ASP cc_start: 0.8958 (p0) cc_final: 0.8186 (p0) REVERT: D 472 GLN cc_start: 0.8589 (mt0) cc_final: 0.8128 (mm-40) REVERT: D 479 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8439 (mt-10) REVERT: D 483 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 497 TYR cc_start: 0.8764 (m-80) cc_final: 0.8380 (m-80) REVERT: D 582 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.8034 (mmm160) REVERT: D 603 PHE cc_start: 0.8766 (t80) cc_final: 0.8321 (t80) outliers start: 18 outliers final: 10 residues processed: 113 average time/residue: 0.4884 time to fit residues: 57.7996 Evaluate side-chains 110 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 467 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.100649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077577 restraints weight = 12234.879| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.83 r_work: 0.2923 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6758 Z= 0.136 Angle : 0.594 8.910 9199 Z= 0.295 Chirality : 0.042 0.163 976 Planarity : 0.003 0.029 1179 Dihedral : 3.920 16.195 865 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.86 % Allowed : 21.32 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.26 (0.30), residues: 792 helix: 1.51 (0.26), residues: 411 sheet: 0.65 (0.75), residues: 43 loop : 0.12 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.012 0.001 TYR D 41 PHE 0.014 0.001 PHE D 369 TRP 0.015 0.001 TRP D 478 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6745) covalent geometry : angle 0.58972 / 0.29 ( 9166) SS BOND : bond 0.00507 / 0.31 ( 6) SS BOND : angle 1.11226 / 0.67 ( 12) hydrogen bonds : bond 0.04438 / 2.93 ( 321) hydrogen bonds : angle 4.52099 / 3.16 ( 984) link_NAG-ASN : bond 0.00203 / 0.07 ( 7) link_NAG-ASN : angle 1.43042 / 1.07 ( 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 116 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8669 (ptm160) cc_final: 0.8059 (ttt90) REVERT: A 465 GLU cc_start: 0.8639 (tt0) cc_final: 0.8253 (tt0) REVERT: D 26 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8214 (mttm) REVERT: D 115 ARG cc_start: 0.8660 (tpm170) cc_final: 0.8421 (tpm170) REVERT: D 213 ASP cc_start: 0.9071 (t70) cc_final: 0.8725 (t0) REVERT: D 243 TYR cc_start: 0.8823 (t80) cc_final: 0.8583 (t80) REVERT: D 287 GLN cc_start: 0.8712 (mp10) cc_final: 0.8284 (pm20) REVERT: D 305 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8454 (tm-30) REVERT: D 467 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: D 471 ASP cc_start: 0.8932 (p0) cc_final: 0.8047 (p0) REVERT: D 472 GLN cc_start: 0.8571 (mt0) cc_final: 0.8100 (mm-40) REVERT: D 483 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8278 (tm-30) REVERT: D 497 TYR cc_start: 0.8769 (m-80) cc_final: 0.8422 (m-80) REVERT: D 582 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.8138 (mmm160) REVERT: D 603 PHE cc_start: 0.8771 (t80) cc_final: 0.8300 (t80) outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 0.4448 time to fit residues: 51.9112 Evaluate side-chains 112 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 467 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.099118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076065 restraints weight = 12158.620| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.83 r_work: 0.2906 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6758 Z= 0.177 Angle : 0.642 12.501 9199 Z= 0.318 Chirality : 0.043 0.159 976 Planarity : 0.004 0.028 1179 Dihedral : 4.076 16.391 865 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.15 % Allowed : 21.03 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.28 (0.29), residues: 792 helix: 1.45 (0.26), residues: 410 sheet: 0.68 (0.75), residues: 43 loop : 0.26 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.012 0.001 TYR D 41 PHE 0.015 0.001 PHE D 369 TRP 0.022 0.001 TRP D 478 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 6745) covalent geometry : angle 0.63846 / 0.32 ( 9166) SS BOND : bond 0.00524 / 0.33 ( 6) SS BOND : angle 1.09512 / 0.65 ( 12) hydrogen bonds : bond 0.04735 / 3.13 ( 321) hydrogen bonds : angle 4.59665 / 3.21 ( 984) link_NAG-ASN : bond 0.00224 / 0.11 ( 7) link_NAG-ASN : angle 1.49064 / 1.12 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2319.79 seconds wall clock time: 40 minutes 26.81 seconds (2426.81 seconds total)