Starting phenix.real_space_refine on Wed Jan 15 00:39:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y0y_38823/01_2025/8y0y_38823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y0y_38823/01_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_38823/01_2025/8y0y_38823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y0y_38823/01_2025/8y0y_38823.map" model { file = "/net/cci-nas-00/data/ceres_data/8y0y_38823/01_2025/8y0y_38823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y0y_38823/01_2025/8y0y_38823.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 3.74, per 1000 atoms: 0.74 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: 1.37 Conformation dependent library (CDL) restraints added in 701.6 milliseconds 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: 0.84 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: 1.69 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.610 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.950 ------------------------------------------------------------------------------- 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 5149 Z= 0.112 Angle : 0.449 5.789 6990 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP E 343 HIS 0.001 0.000 HIS D 60 PHE 0.005 0.001 PHE A 490 TYR 0.006 0.001 TYR E 210 ARG 0.003 0.000 ARG E 222 *********************** 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 : 0.612 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 1.1944 time to fit residues: 101.4134 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 : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.166026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141018 restraints weight = 5943.355| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.02 r_work: 0.3627 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5149 Z= 0.166 Angle : 0.598 12.668 6990 Z= 0.316 Chirality : 0.046 0.242 752 Planarity : 0.004 0.036 905 Dihedral : 4.095 25.045 736 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.03 % Allowed : 9.06 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.33), residues: 642 helix: -2.75 (0.99), residues: 21 sheet: 1.12 (0.35), residues: 244 loop : -0.89 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS E 407 PHE 0.011 0.001 PHE A 377 TYR 0.017 0.001 TYR E 210 ARG 0.003 0.000 ARG A 466 *********************** 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 76 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.520 Fit side-chains REVERT: E 253 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7833 (p0) REVERT: E 379 MET cc_start: 0.7236 (ptt) cc_final: 0.6980 (ptt) REVERT: D 90 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8012 (tptt) REVERT: A 378 LYS cc_start: 0.6275 (pttp) cc_final: 0.6061 (ptpp) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 1.2134 time to fit residues: 91.7070 Evaluate side-chains 69 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.158775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133728 restraints weight = 5974.467| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.99 r_work: 0.3546 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5149 Z= 0.229 Angle : 0.642 10.328 6990 Z= 0.344 Chirality : 0.048 0.200 752 Planarity : 0.005 0.040 905 Dihedral : 4.493 20.149 736 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.07 % Allowed : 9.24 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.33), residues: 642 helix: -3.15 (0.90), residues: 21 sheet: 1.14 (0.34), residues: 249 loop : -1.21 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS D 60 PHE 0.011 0.002 PHE A 377 TYR 0.016 0.002 TYR E 210 ARG 0.004 0.001 ARG A 466 *********************** 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 83 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.587 Fit side-chains REVERT: E 253 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7088 (t0) REVERT: E 299 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7517 (mm110) REVERT: E 342 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: D 90 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8095 (tptt) REVERT: D 449 ASP cc_start: 0.6583 (m-30) cc_final: 0.6265 (m-30) REVERT: D 493 ARG cc_start: 0.7345 (mtm110) cc_final: 0.6961 (mtm-85) REVERT: D 537 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7754 (pm20) outliers start: 22 outliers final: 10 residues processed: 74 average time/residue: 1.1761 time to fit residues: 91.0476 Evaluate side-chains 69 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 35 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 380 ASN E 411 GLN D 82 ASN D 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.157062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131383 restraints weight = 6045.966| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.03 r_work: 0.3514 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5149 Z= 0.244 Angle : 0.643 9.768 6990 Z= 0.346 Chirality : 0.048 0.189 752 Planarity : 0.005 0.045 905 Dihedral : 4.593 18.283 736 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.18 % Allowed : 9.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.32), residues: 642 helix: -3.07 (0.76), residues: 27 sheet: 0.89 (0.33), residues: 252 loop : -1.38 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 436 HIS 0.004 0.001 HIS D 60 PHE 0.009 0.002 PHE E 364 TYR 0.016 0.002 TYR E 391 ARG 0.003 0.000 ARG A 466 *********************** 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 86 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.531 Fit side-chains REVERT: E 250 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8089 (pp30) REVERT: E 253 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7128 (t0) REVERT: E 299 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7569 (mm110) REVERT: E 342 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: D 449 ASP cc_start: 0.6582 (m-30) cc_final: 0.6297 (m-30) REVERT: D 493 ARG cc_start: 0.7385 (mtm110) cc_final: 0.6943 (mtm-85) REVERT: D 535 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7926 (tptm) REVERT: A 378 LYS cc_start: 0.7065 (ptpp) cc_final: 0.6640 (ptpt) REVERT: A 382 VAL cc_start: 0.6251 (OUTLIER) cc_final: 0.5928 (p) REVERT: A 455 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7700 (tt) outliers start: 28 outliers final: 11 residues processed: 75 average time/residue: 1.1295 time to fit residues: 89.1345 Evaluate side-chains 75 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 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 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.158687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133126 restraints weight = 5922.779| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.02 r_work: 0.3529 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5149 Z= 0.184 Angle : 0.589 9.129 6990 Z= 0.317 Chirality : 0.046 0.167 752 Planarity : 0.005 0.046 905 Dihedral : 4.382 17.813 736 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.18 % Allowed : 11.46 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.32), residues: 642 helix: -2.88 (0.79), residues: 27 sheet: 0.67 (0.33), residues: 263 loop : -1.35 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 60 PHE 0.008 0.001 PHE A 400 TYR 0.013 0.002 TYR E 210 ARG 0.002 0.000 ARG E 222 *********************** 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 83 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.584 Fit side-chains REVERT: E 250 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8114 (pp30) REVERT: E 253 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7362 (t0) REVERT: E 299 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7513 (mm110) REVERT: E 398 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8136 (mt) REVERT: E 411 GLN cc_start: 0.6652 (OUTLIER) cc_final: 0.6141 (pt0) REVERT: D 449 ASP cc_start: 0.6329 (m-30) cc_final: 0.6093 (m-30) REVERT: D 535 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7841 (tptm) REVERT: A 382 VAL cc_start: 0.6207 (OUTLIER) cc_final: 0.5963 (p) REVERT: A 455 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7689 (tt) outliers start: 28 outliers final: 15 residues processed: 76 average time/residue: 1.1728 time to fit residues: 93.2318 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 : 0.597 ------------------------------------------------------------------------------- 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 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 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 405 ASP 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 26 optimal weight: 0.1980 chunk 54 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN D 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134521 restraints weight = 5947.960| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.04 r_work: 0.3544 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5149 Z= 0.144 Angle : 0.535 7.708 6990 Z= 0.288 Chirality : 0.044 0.155 752 Planarity : 0.004 0.044 905 Dihedral : 4.070 16.481 736 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.81 % Allowed : 13.12 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.33), residues: 642 helix: -2.17 (0.99), residues: 21 sheet: 0.73 (0.33), residues: 262 loop : -1.28 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 60 PHE 0.007 0.001 PHE A 400 TYR 0.013 0.001 TYR E 210 ARG 0.003 0.000 ARG E 222 *********************** 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 76 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.537 Fit side-chains REVERT: E 253 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7703 (t0) REVERT: E 342 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: E 398 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8097 (mt) REVERT: E 411 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6094 (pt0) REVERT: D 59 MET cc_start: 0.7996 (mmm) cc_final: 0.7524 (mmm) REVERT: D 449 ASP cc_start: 0.6400 (m-30) cc_final: 0.6120 (m-30) REVERT: D 535 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7811 (tptm) REVERT: A 378 LYS cc_start: 0.6837 (ptpp) cc_final: 0.6460 (ptmt) REVERT: A 455 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7654 (tt) outliers start: 26 outliers final: 13 residues processed: 68 average time/residue: 1.1018 time to fit residues: 78.6794 Evaluate side-chains 65 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER 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 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 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 535 LYS Chi-restraints excluded: chain A residue 341 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 D 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127685 restraints weight = 5909.922| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.02 r_work: 0.3520 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5149 Z= 0.361 Angle : 0.742 10.867 6990 Z= 0.399 Chirality : 0.051 0.184 752 Planarity : 0.006 0.054 905 Dihedral : 4.995 20.556 736 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.99 % Allowed : 13.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.33), residues: 642 helix: -2.75 (0.96), residues: 21 sheet: 0.61 (0.32), residues: 269 loop : -1.59 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.007 0.002 HIS D 60 PHE 0.013 0.002 PHE A 377 TYR 0.018 0.003 TYR A 495 ARG 0.004 0.001 ARG D 97 *********************** 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 81 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.590 Fit side-chains REVERT: E 299 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7547 (mm110) REVERT: E 342 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: E 398 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8185 (mt) REVERT: E 411 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6061 (pt0) REVERT: D 449 ASP cc_start: 0.6786 (m-30) cc_final: 0.6491 (m-30) REVERT: D 535 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7974 (tptm) REVERT: A 455 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7766 (tt) outliers start: 27 outliers final: 16 residues processed: 73 average time/residue: 1.0003 time to fit residues: 77.1695 Evaluate side-chains 76 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER 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 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 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 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 0.0010 chunk 10 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 411 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131923 restraints weight = 5930.088| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.02 r_work: 0.3564 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5149 Z= 0.179 Angle : 0.611 11.276 6990 Z= 0.322 Chirality : 0.046 0.158 752 Planarity : 0.005 0.051 905 Dihedral : 4.421 18.496 736 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.25 % Allowed : 13.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.33), residues: 642 helix: -2.46 (1.01), residues: 21 sheet: 0.52 (0.32), residues: 274 loop : -1.54 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS D 60 PHE 0.008 0.001 PHE A 400 TYR 0.014 0.001 TYR E 391 ARG 0.002 0.000 ARG E 222 *********************** 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 78 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.542 Fit side-chains REVERT: E 253 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7453 (t0) REVERT: E 342 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: E 398 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8136 (mt) REVERT: D 449 ASP cc_start: 0.6391 (m-30) cc_final: 0.6108 (m-30) REVERT: D 535 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7866 (tptm) REVERT: A 455 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7703 (tt) outliers start: 23 outliers final: 15 residues processed: 71 average time/residue: 1.0836 time to fit residues: 80.7712 Evaluate side-chains 68 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER 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 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 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 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 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 D 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130228 restraints weight = 5945.776| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.02 r_work: 0.3496 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5149 Z= 0.227 Angle : 0.644 10.234 6990 Z= 0.341 Chirality : 0.047 0.167 752 Planarity : 0.005 0.053 905 Dihedral : 4.553 18.398 736 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.33), residues: 642 helix: -2.49 (1.01), residues: 21 sheet: 0.51 (0.32), residues: 275 loop : -1.55 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS D 60 PHE 0.009 0.001 PHE E 364 TYR 0.014 0.002 TYR E 391 ARG 0.004 0.000 ARG E 222 *********************** 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 75 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.585 Fit side-chains REVERT: E 253 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7155 (t0) REVERT: E 299 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7527 (mm110) REVERT: E 342 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: E 398 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8137 (mt) REVERT: E 411 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6369 (pt0) REVERT: D 449 ASP cc_start: 0.6450 (m-30) cc_final: 0.6182 (m-30) REVERT: D 535 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7864 (tptm) REVERT: A 378 LYS cc_start: 0.6791 (ptpp) cc_final: 0.6503 (ptpt) REVERT: A 455 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7712 (tt) outliers start: 25 outliers final: 17 residues processed: 68 average time/residue: 1.0871 time to fit residues: 77.8253 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 : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 D 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.158363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133077 restraints weight = 5903.131| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.01 r_work: 0.3577 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5149 Z= 0.159 Angle : 0.577 9.642 6990 Z= 0.305 Chirality : 0.045 0.149 752 Planarity : 0.005 0.050 905 Dihedral : 4.237 17.535 736 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.44 % Allowed : 14.05 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.33), residues: 642 helix: -2.39 (1.01), residues: 21 sheet: 0.62 (0.33), residues: 260 loop : -1.43 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 60 PHE 0.008 0.001 PHE A 400 TYR 0.014 0.001 TYR E 210 ARG 0.003 0.000 ARG E 222 ********************** 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 73 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.600 Fit side-chains REVERT: E 253 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7549 (t0) REVERT: E 342 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: E 398 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8111 (mt) REVERT: E 411 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.6047 (pt0) REVERT: D 59 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7561 (mmm) REVERT: D 449 ASP cc_start: 0.6411 (m-30) cc_final: 0.6107 (m-30) REVERT: D 535 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7876 (tptm) REVERT: A 378 LYS cc_start: 0.6710 (ptpp) cc_final: 0.6274 (ptmt) REVERT: A 455 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7639 (tt) outliers start: 24 outliers final: 15 residues processed: 65 average time/residue: 1.0272 time to fit residues: 70.5975 Evaluate side-chains 69 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 SER 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 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 59 MET 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 48 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128760 restraints weight = 6030.424| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.02 r_work: 0.3476 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5149 Z= 0.289 Angle : 0.690 9.757 6990 Z= 0.367 Chirality : 0.049 0.175 752 Planarity : 0.005 0.054 905 Dihedral : 4.765 19.231 736 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.25 % Allowed : 14.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.33), residues: 642 helix: -2.64 (1.01), residues: 21 sheet: 0.50 (0.33), residues: 270 loop : -1.57 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 436 HIS 0.005 0.002 HIS D 60 PHE 0.010 0.002 PHE D 530 TYR 0.015 0.002 TYR A 495 ARG 0.003 0.000 ARG E 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.74 seconds wall clock time: 67 minutes 33.40 seconds (4053.40 seconds total)