Starting phenix.real_space_refine on Fri Aug 22 20:28:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y0y_38823/08_2025/8y0y_38823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y0y_38823/08_2025/8y0y_38823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y0y_38823/08_2025/8y0y_38823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y0y_38823/08_2025/8y0y_38823.map" model { file = "/net/cci-nas-00/data/ceres_data/8y0y_38823/08_2025/8y0y_38823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y0y_38823/08_2025/8y0y_38823.cif" } resolution = 2.86 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= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3253 atoms to isotropic. 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 24 5.16 5 C 3177 2.51 5 N 849 2.21 5 O 977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5027 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1729 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1741 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain breaks: 1 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.39, per 1000 atoms: 0.28 Number of scatterers: 5027 At special positions: 0 Unit cell: (84.7, 99, 90.2, 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 24 16.00 O 977 8.00 N 849 7.00 C 3177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 184 " - pdb=" SG CYS E 249 " distance=2.03 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 121 " distance=2.03 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 520 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 A 601 " - " ASN A 343 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 159.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1174 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 13 sheets defined 9.2% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'E' and resid 240 through 244 removed outlier: 4.205A pdb=" N PHE E 244 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.600A pdb=" N TYR E 328 " --> pdb=" O PHE E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 4.162A pdb=" N THR E 387 " --> pdb=" O ALA E 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 removed outlier: 4.010A pdb=" N ASN D 56 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR D 57 " --> pdb=" O PHE D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 57' Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.697A pdb=" N THR D 116 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.879A pdb=" N SER D 515 " --> pdb=" O PRO D 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.254A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.712A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'E' and resid 167 through 168 removed outlier: 3.715A pdb=" N VAL E 180 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP E 231 " --> pdb=" O SER E 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 171 through 174 removed outlier: 6.639A pdb=" N TRP E 196 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 299 through 303 removed outlier: 3.553A pdb=" N GLN E 299 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 321 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 303 " --> pdb=" O SER E 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'E' and resid 354 through 356 removed outlier: 5.018A pdb=" N TRP E 343 " --> pdb=" O ARG E 334 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG E 334 " --> pdb=" O TRP E 343 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 331 " --> pdb=" O ALA E 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 354 through 356 removed outlier: 5.018A pdb=" N TRP E 343 " --> pdb=" O ARG E 334 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG E 334 " --> pdb=" O TRP E 343 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 331 " --> pdb=" O ALA E 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AA8, first strand: chain 'D' and resid 36 through 37 removed outlier: 7.260A pdb=" N MET D 59 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL D 75 " --> pdb=" O MET D 59 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP D 61 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 438 through 439 removed outlier: 3.701A pdb=" N PHE D 503 " --> pdb=" O CYS D 455 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP D 502 " --> pdb=" O SER D 499 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 442 through 445 removed outlier: 3.699A pdb=" N GLU D 537 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 445 " --> pdb=" O GLU D 537 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU D 465 " --> pdb=" O TYR D 481 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR D 481 " --> pdb=" O LEU D 465 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP D 467 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.687A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.585A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 414 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: 0.59 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1621 1.35 - 1.47: 1367 1.47 - 1.59: 2129 1.59 - 1.71: 0 1.71 - 1.83: 32 Bond restraints: 5149 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.75e-01 bond pdb=" CG PRO E 169 " pdb=" CD PRO E 169 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.37e-01 bond pdb=" C LEU D 526 " pdb=" N PRO D 527 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.59e-01 ... (remaining 5144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 6807 1.16 - 2.32: 146 2.32 - 3.47: 31 3.47 - 4.63: 4 4.63 - 5.79: 2 Bond angle restraints: 6990 Sorted by residual: angle pdb=" N GLY E 412 " pdb=" CA GLY E 412 " pdb=" C GLY E 412 " ideal model delta sigma weight residual 112.48 115.58 -3.10 1.21e+00 6.83e-01 6.58e+00 angle pdb=" C ASN D 525 " pdb=" N LEU D 526 " pdb=" CA LEU D 526 " ideal model delta sigma weight residual 120.26 123.23 -2.97 1.34e+00 5.57e-01 4.90e+00 angle pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " ideal model delta sigma weight residual 116.30 122.09 -5.79 3.50e+00 8.16e-02 2.74e+00 angle pdb=" CA GLY E 412 " pdb=" C GLY E 412 " pdb=" O GLY E 412 " ideal model delta sigma weight residual 122.24 120.82 1.42 8.70e-01 1.32e+00 2.66e+00 angle pdb=" CA PRO D 39 " pdb=" CB PRO D 39 " pdb=" CG PRO D 39 " ideal model delta sigma weight residual 104.50 107.29 -2.79 1.90e+00 2.77e-01 2.16e+00 ... (remaining 6985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 2767 16.05 - 32.11: 200 32.11 - 48.16: 47 48.16 - 64.22: 12 64.22 - 80.27: 6 Dihedral angle restraints: 3032 sinusoidal: 1170 harmonic: 1862 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 47.49 45.51 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" CA ASP D 524 " pdb=" CB ASP D 524 " pdb=" CG ASP D 524 " pdb=" OD1 ASP D 524 " ideal model delta sinusoidal sigma weight residual -30.00 -84.49 54.49 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CB LYS E 206 " pdb=" CG LYS E 206 " pdb=" CD LYS E 206 " pdb=" CE LYS E 206 " ideal model delta sinusoidal sigma weight residual 60.00 116.48 -56.48 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 3029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 417 0.025 - 0.049: 205 0.049 - 0.074: 59 0.074 - 0.098: 31 0.098 - 0.123: 40 Chirality restraints: 752 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CB ILE E 163 " pdb=" CA ILE E 163 " pdb=" CG1 ILE E 163 " pdb=" CG2 ILE E 163 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE D 480 " pdb=" N ILE D 480 " pdb=" C ILE D 480 " pdb=" CB ILE D 480 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 749 not shown) Planarity restraints: 906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 309 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO E 310 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 310 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 310 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 134 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO D 135 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 135 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 135 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 38 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO D 39 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " -0.017 5.00e-02 4.00e+02 ... (remaining 903 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1467 2.81 - 3.34: 3744 3.34 - 3.86: 7623 3.86 - 4.38: 8663 4.38 - 4.90: 16227 Nonbonded interactions: 37724 Sorted by model distance: nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.292 3.040 nonbonded pdb=" OG SER E 345 " pdb=" O TYR E 355 " model vdw 2.320 3.040 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.353 3.040 nonbonded pdb=" OE2 GLU E 404 " pdb=" ND2 ASN A 450 " model vdw 2.368 3.120 nonbonded pdb=" O PHE D 54 " pdb=" NH2 ARG D 97 " model vdw 2.428 3.120 ... (remaining 37719 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.040 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:5.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 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 : 0.002 0.027 5158 Z= 0.098 Angle : 0.450 5.789 7009 Z= 0.246 Chirality : 0.041 0.123 752 Planarity : 0.004 0.037 905 Dihedral : 12.370 80.272 1834 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.18 % Allowed : 0.37 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: 0.04 (0.33), residues: 642 helix: -2.71 (0.98), residues: 19 sheet: 1.30 (0.35), residues: 235 loop : -0.66 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 222 TYR 0.006 0.001 TYR E 210 PHE 0.005 0.001 PHE A 490 TRP 0.005 0.001 TRP E 343 HIS 0.001 0.000 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00179 ( 5149) covalent geometry : angle 0.44885 ( 6990) SS BOND : bond 0.00313 ( 8) SS BOND : angle 0.75450 ( 16) hydrogen bonds : bond 0.29114 ( 157) hydrogen bonds : angle 9.27533 ( 414) link_NAG-ASN : bond 0.00299 ( 1) link_NAG-ASN : angle 0.55955 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.149 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.4397 time to fit residues: 37.2078 Evaluate side-chains 60 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 0.0870 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN E 373 ASN E 411 GLN D 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139586 restraints weight = 5960.021| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.03 r_work: 0.3610 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5158 Z= 0.124 Angle : 0.627 11.616 7009 Z= 0.331 Chirality : 0.046 0.218 752 Planarity : 0.004 0.037 905 Dihedral : 4.189 24.349 736 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.03 % Allowed : 9.61 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.28 (0.33), residues: 642 helix: -2.85 (0.97), residues: 21 sheet: 1.08 (0.35), residues: 244 loop : -0.93 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.017 0.002 TYR E 210 PHE 0.016 0.001 PHE A 377 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5149) covalent geometry : angle 0.60593 ( 6990) SS BOND : bond 0.00844 ( 8) SS BOND : angle 3.37349 ( 16) hydrogen bonds : bond 0.03764 ( 157) hydrogen bonds : angle 5.79619 ( 414) link_NAG-ASN : bond 0.00272 ( 1) link_NAG-ASN : angle 0.92978 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.208 Fit side-chains REVERT: E 253 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7108 (t0) REVERT: E 379 MET cc_start: 0.7290 (ptt) cc_final: 0.6969 (ptt) REVERT: D 90 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8026 (tptt) outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 0.4716 time to fit residues: 35.0466 Evaluate side-chains 64 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 380 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 47 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN E 373 ASN E 407 HIS E 411 GLN D 102 ASN A 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133878 restraints weight = 5940.868| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.99 r_work: 0.3548 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5158 Z= 0.152 Angle : 0.657 10.440 7009 Z= 0.349 Chirality : 0.047 0.174 752 Planarity : 0.005 0.040 905 Dihedral : 4.472 19.894 736 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.25 % Allowed : 9.24 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.49 (0.33), residues: 642 helix: -3.13 (0.91), residues: 21 sheet: 1.05 (0.34), residues: 252 loop : -1.21 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.014 0.002 TYR E 210 PHE 0.010 0.002 PHE A 377 TRP 0.009 0.002 TRP A 436 HIS 0.005 0.002 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5149) covalent geometry : angle 0.63745 ( 6990) SS BOND : bond 0.00633 ( 8) SS BOND : angle 3.33005 ( 16) hydrogen bonds : bond 0.04512 ( 157) hydrogen bonds : angle 5.65757 ( 414) link_NAG-ASN : bond 0.00139 ( 1) link_NAG-ASN : angle 1.19970 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.128 Fit side-chains REVERT: E 253 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7074 (t0) REVERT: E 299 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7656 (mm110) REVERT: E 342 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: D 90 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8097 (tptt) REVERT: D 449 ASP cc_start: 0.6566 (m-30) cc_final: 0.6249 (m-30) REVERT: D 493 ARG cc_start: 0.7330 (mtm110) cc_final: 0.6960 (mtm-85) REVERT: D 537 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7769 (pm20) outliers start: 23 outliers final: 10 residues processed: 77 average time/residue: 0.4513 time to fit residues: 36.3467 Evaluate side-chains 72 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 188 GLN E 214 ASN E 373 ASN E 411 GLN D 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.158483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132904 restraints weight = 5956.290| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.02 r_work: 0.3526 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5158 Z= 0.138 Angle : 0.618 9.261 7009 Z= 0.331 Chirality : 0.046 0.172 752 Planarity : 0.005 0.042 905 Dihedral : 4.393 17.599 736 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.55 % Allowed : 9.61 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.70 (0.32), residues: 642 helix: -2.98 (0.79), residues: 27 sheet: 0.92 (0.34), residues: 252 loop : -1.34 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.015 0.002 TYR E 391 PHE 0.008 0.001 PHE E 364 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5149) covalent geometry : angle 0.59921 ( 6990) SS BOND : bond 0.00570 ( 8) SS BOND : angle 3.16639 ( 16) hydrogen bonds : bond 0.04145 ( 157) hydrogen bonds : angle 5.49513 ( 414) link_NAG-ASN : bond 0.00174 ( 1) link_NAG-ASN : angle 1.25425 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.189 Fit side-chains REVERT: E 250 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: E 253 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7240 (t0) REVERT: E 299 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7597 (mm110) REVERT: E 342 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: D 68 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7536 (mptt) REVERT: D 449 ASP cc_start: 0.6413 (m-30) cc_final: 0.6142 (m-30) REVERT: D 493 ARG cc_start: 0.7366 (mtm110) cc_final: 0.6964 (mtm-85) REVERT: D 535 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7827 (tptm) REVERT: A 382 VAL cc_start: 0.6181 (OUTLIER) cc_final: 0.5893 (p) REVERT: A 455 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7696 (tt) outliers start: 30 outliers final: 10 residues processed: 78 average time/residue: 0.4767 time to fit residues: 38.9371 Evaluate side-chains 74 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 250 GLN Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN E 373 ASN D 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133097 restraints weight = 6017.917| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.03 r_work: 0.3532 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5158 Z= 0.123 Angle : 0.593 8.717 7009 Z= 0.318 Chirality : 0.045 0.157 752 Planarity : 0.004 0.042 905 Dihedral : 4.284 17.245 736 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.99 % Allowed : 11.28 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.69 (0.32), residues: 642 helix: -2.71 (0.93), residues: 21 sheet: 0.91 (0.33), residues: 251 loop : -1.37 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.014 0.001 TYR E 210 PHE 0.008 0.001 PHE A 400 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5149) covalent geometry : angle 0.57558 ( 6990) SS BOND : bond 0.00553 ( 8) SS BOND : angle 3.02223 ( 16) hydrogen bonds : bond 0.03872 ( 157) hydrogen bonds : angle 5.38053 ( 414) link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 1.30232 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.167 Fit side-chains REVERT: E 250 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8103 (pp30) REVERT: E 253 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7345 (t0) REVERT: E 342 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: E 398 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8123 (mt) REVERT: E 411 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6165 (pt0) REVERT: D 59 MET cc_start: 0.8080 (mmm) cc_final: 0.7635 (mmm) REVERT: D 68 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7486 (mptt) REVERT: D 449 ASP cc_start: 0.6320 (m-30) cc_final: 0.6044 (m-30) REVERT: D 493 ARG cc_start: 0.7391 (mtm110) cc_final: 0.6964 (mtm-85) REVERT: D 535 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7856 (tptm) REVERT: A 382 VAL cc_start: 0.6169 (OUTLIER) cc_final: 0.5926 (p) REVERT: A 455 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7721 (tt) outliers start: 27 outliers final: 14 residues processed: 74 average time/residue: 0.5006 time to fit residues: 38.7350 Evaluate side-chains 76 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 250 GLN Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 MET Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 521 GLN Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN E 411 GLN D 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131684 restraints weight = 5986.823| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.03 r_work: 0.3510 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5158 Z= 0.145 Angle : 0.628 9.059 7009 Z= 0.337 Chirality : 0.046 0.161 752 Planarity : 0.005 0.045 905 Dihedral : 4.444 18.154 736 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.81 % Allowed : 12.20 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.85 (0.32), residues: 642 helix: -2.69 (0.92), residues: 21 sheet: 0.60 (0.33), residues: 263 loop : -1.39 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 222 TYR 0.014 0.002 TYR E 210 PHE 0.010 0.001 PHE A 377 TRP 0.010 0.002 TRP A 436 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5149) covalent geometry : angle 0.60964 ( 6990) SS BOND : bond 0.00673 ( 8) SS BOND : angle 3.16771 ( 16) hydrogen bonds : bond 0.04163 ( 157) hydrogen bonds : angle 5.47405 ( 414) link_NAG-ASN : bond 0.00158 ( 1) link_NAG-ASN : angle 1.31215 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.193 Fit side-chains REVERT: E 250 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8067 (pp30) REVERT: E 253 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7152 (t0) REVERT: E 299 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7408 (mm110) REVERT: E 342 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: E 398 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8127 (mt) REVERT: D 68 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7538 (mptt) REVERT: D 449 ASP cc_start: 0.6424 (m-30) cc_final: 0.6144 (m-30) REVERT: D 535 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7883 (tptm) REVERT: A 382 VAL cc_start: 0.6029 (OUTLIER) cc_final: 0.5821 (p) REVERT: A 455 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7686 (tt) outliers start: 26 outliers final: 16 residues processed: 78 average time/residue: 0.4922 time to fit residues: 40.2144 Evaluate side-chains 79 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 250 GLN Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 MET Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 521 GLN Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN E 380 ASN D 28 GLN D 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131018 restraints weight = 5966.403| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.02 r_work: 0.3505 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5158 Z= 0.160 Angle : 0.670 11.071 7009 Z= 0.352 Chirality : 0.047 0.166 752 Planarity : 0.005 0.049 905 Dihedral : 4.552 18.544 736 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.55 % Allowed : 12.57 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.90 (0.33), residues: 642 helix: -2.48 (0.99), residues: 21 sheet: 0.56 (0.33), residues: 263 loop : -1.43 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 222 TYR 0.014 0.002 TYR A 495 PHE 0.010 0.001 PHE A 377 TRP 0.010 0.002 TRP A 436 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5149) covalent geometry : angle 0.65184 ( 6990) SS BOND : bond 0.00701 ( 8) SS BOND : angle 3.22186 ( 16) hydrogen bonds : bond 0.04304 ( 157) hydrogen bonds : angle 5.55482 ( 414) link_NAG-ASN : bond 0.00147 ( 1) link_NAG-ASN : angle 1.38873 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.116 Fit side-chains REVERT: E 250 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8075 (pp30) REVERT: E 253 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7116 (t0) REVERT: E 299 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7356 (mm110) REVERT: E 342 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: E 398 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8143 (mt) REVERT: E 411 GLN cc_start: 0.6722 (OUTLIER) cc_final: 0.6219 (pt0) REVERT: D 68 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7589 (mptt) REVERT: D 449 ASP cc_start: 0.6474 (m-30) cc_final: 0.6205 (m-30) REVERT: D 535 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7927 (tptm) REVERT: A 382 VAL cc_start: 0.6013 (OUTLIER) cc_final: 0.5799 (p) REVERT: A 455 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7725 (tt) outliers start: 30 outliers final: 18 residues processed: 75 average time/residue: 0.4590 time to fit residues: 36.0256 Evaluate side-chains 80 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 250 GLN Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 MET Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 521 GLN Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 59 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN D 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.157217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131690 restraints weight = 6029.438| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.03 r_work: 0.3511 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5158 Z= 0.135 Angle : 0.629 10.121 7009 Z= 0.331 Chirality : 0.046 0.158 752 Planarity : 0.005 0.048 905 Dihedral : 4.397 18.112 736 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.18 % Allowed : 13.12 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.87 (0.33), residues: 642 helix: -2.30 (1.03), residues: 21 sheet: 0.60 (0.32), residues: 274 loop : -1.50 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 222 TYR 0.014 0.002 TYR E 391 PHE 0.008 0.001 PHE A 400 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5149) covalent geometry : angle 0.61207 ( 6990) SS BOND : bond 0.00611 ( 8) SS BOND : angle 3.04115 ( 16) hydrogen bonds : bond 0.03960 ( 157) hydrogen bonds : angle 5.41918 ( 414) link_NAG-ASN : bond 0.00170 ( 1) link_NAG-ASN : angle 1.43986 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.133 Fit side-chains REVERT: E 250 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: E 253 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7294 (t0) REVERT: E 299 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7415 (mm110) REVERT: E 342 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: E 398 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8125 (mt) REVERT: E 411 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.6038 (pt0) REVERT: D 68 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7595 (mptt) REVERT: D 449 ASP cc_start: 0.6371 (m-30) cc_final: 0.6103 (m-30) REVERT: D 535 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7840 (tptm) REVERT: A 455 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7701 (tt) outliers start: 28 outliers final: 15 residues processed: 73 average time/residue: 0.4278 time to fit residues: 32.7860 Evaluate side-chains 72 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 250 GLN Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 MET Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 521 GLN Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130409 restraints weight = 5957.015| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.03 r_work: 0.3495 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5158 Z= 0.154 Angle : 0.656 9.285 7009 Z= 0.348 Chirality : 0.047 0.166 752 Planarity : 0.005 0.049 905 Dihedral : 4.545 18.421 736 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.62 % Allowed : 14.05 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.91 (0.33), residues: 642 helix: -2.34 (1.05), residues: 21 sheet: 0.55 (0.32), residues: 275 loop : -1.52 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.014 0.002 TYR E 391 PHE 0.009 0.001 PHE E 364 TRP 0.010 0.002 TRP A 436 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5149) covalent geometry : angle 0.63927 ( 6990) SS BOND : bond 0.00697 ( 8) SS BOND : angle 3.13902 ( 16) hydrogen bonds : bond 0.04229 ( 157) hydrogen bonds : angle 5.53423 ( 414) link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 1.40460 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 0.121 Fit side-chains REVERT: E 250 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8072 (pp30) REVERT: E 253 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7111 (t0) REVERT: E 299 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7377 (mm110) REVERT: E 342 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: E 398 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8132 (mt) REVERT: E 411 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6114 (pt0) REVERT: D 68 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7559 (mptt) REVERT: D 449 ASP cc_start: 0.6428 (m-30) cc_final: 0.6152 (m-30) REVERT: D 535 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7928 (tptm) REVERT: A 455 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7719 (tt) outliers start: 25 outliers final: 15 residues processed: 71 average time/residue: 0.4448 time to fit residues: 33.1335 Evaluate side-chains 74 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 250 GLN Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 MET Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 521 GLN Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 28 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN E 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132515 restraints weight = 5936.032| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.03 r_work: 0.3516 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5158 Z= 0.115 Angle : 0.596 9.025 7009 Z= 0.313 Chirality : 0.045 0.155 752 Planarity : 0.005 0.045 905 Dihedral : 4.263 17.570 736 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.81 % Allowed : 14.05 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.83 (0.33), residues: 642 helix: -2.26 (1.03), residues: 21 sheet: 0.66 (0.33), residues: 272 loop : -1.50 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 222 TYR 0.013 0.001 TYR E 391 PHE 0.008 0.001 PHE A 400 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5149) covalent geometry : angle 0.58039 ( 6990) SS BOND : bond 0.00513 ( 8) SS BOND : angle 2.82254 ( 16) hydrogen bonds : bond 0.03625 ( 157) hydrogen bonds : angle 5.32812 ( 414) link_NAG-ASN : bond 0.00216 ( 1) link_NAG-ASN : angle 1.41364 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.167 Fit side-chains REVERT: E 250 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8116 (pp30) REVERT: E 253 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7540 (t0) REVERT: E 299 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7345 (mm110) REVERT: E 342 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: E 398 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8110 (mt) REVERT: D 59 MET cc_start: 0.8135 (mmm) cc_final: 0.7633 (mmm) REVERT: D 68 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7512 (mptt) REVERT: D 449 ASP cc_start: 0.6248 (m-30) cc_final: 0.5979 (m-30) REVERT: D 535 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7879 (tptm) REVERT: A 455 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7702 (tt) outliers start: 26 outliers final: 16 residues processed: 69 average time/residue: 0.3975 time to fit residues: 28.9388 Evaluate side-chains 73 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 250 GLN Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 521 GLN Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131223 restraints weight = 5961.610| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.03 r_work: 0.3504 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5158 Z= 0.139 Angle : 0.629 8.728 7009 Z= 0.332 Chirality : 0.046 0.157 752 Planarity : 0.005 0.051 905 Dihedral : 4.400 17.477 736 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.62 % Allowed : 14.23 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 aren not related in a simple way. whole: -0.90 (0.33), residues: 642 helix: -2.33 (1.04), residues: 21 sheet: 0.56 (0.33), residues: 275 loop : -1.51 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 222 TYR 0.014 0.002 TYR E 391 PHE 0.008 0.001 PHE A 400 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5149) covalent geometry : angle 0.61260 ( 6990) SS BOND : bond 0.00637 ( 8) SS BOND : angle 3.01822 ( 16) hydrogen bonds : bond 0.03960 ( 157) hydrogen bonds : angle 5.40073 ( 414) link_NAG-ASN : bond 0.00212 ( 1) link_NAG-ASN : angle 1.38171 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1750.41 seconds wall clock time: 30 minutes 26.76 seconds (1826.76 seconds total)