Starting phenix.real_space_refine on Tue Mar 11 20:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rnx_24582/03_2025/7rnx_24582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rnx_24582/03_2025/7rnx_24582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rnx_24582/03_2025/7rnx_24582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rnx_24582/03_2025/7rnx_24582.map" model { file = "/net/cci-nas-00/data/ceres_data/7rnx_24582/03_2025/7rnx_24582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rnx_24582/03_2025/7rnx_24582.cif" } resolution = 3.42 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= 0.005 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4438 2.51 5 N 1140 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6758 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3379 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "B" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3379 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Time building chain proxies: 4.32, per 1000 atoms: 0.64 Number of scatterers: 6758 At special positions: 0 Unit cell: (76.65, 75.6, 113.4, 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 40 16.00 O 1140 8.00 N 1140 7.00 C 4438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 removed outlier: 3.739A pdb=" N ARG A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 71 removed outlier: 4.182A pdb=" N THR A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 removed outlier: 4.101A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 115 through 118 removed outlier: 3.512A pdb=" N ASP A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 118' Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 127 through 141 Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 170 through 191 removed outlier: 4.144A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 removed outlier: 3.749A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 233 removed outlier: 3.945A pdb=" N ILE A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 3.885A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 4.007A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.972A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 Processing helix chain 'A' and resid 329 through 348 Processing helix chain 'A' and resid 357 through 379 removed outlier: 4.430A pdb=" N LEU A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 393 through 401 removed outlier: 4.369A pdb=" N LEU A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 421 through 438 Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.503A pdb=" N LEU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 32 through 71 removed outlier: 4.124A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 4.389A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 123 through 141 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 148 through 167 removed outlier: 4.126A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 191 removed outlier: 3.719A pdb=" N HIS B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 removed outlier: 3.681A pdb=" N ILE B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.542A pdb=" N VAL B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 removed outlier: 3.516A pdb=" N THR B 251 " --> pdb=" O PRO B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 252 through 280 Proline residue: B 267 - end of helix removed outlier: 4.355A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.936A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.713A pdb=" N THR B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 349 removed outlier: 3.795A pdb=" N VAL B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 379 removed outlier: 4.119A pdb=" N ALA B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 4.020A pdb=" N PHE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 404 through 415 Processing helix chain 'B' and resid 421 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.723A pdb=" N GLN B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1425 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: 1.90 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1714 1.33 - 1.45: 1284 1.45 - 1.57: 3830 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6902 Sorted by residual: bond pdb=" C TYR B 75 " pdb=" N PRO B 76 " ideal model delta sigma weight residual 1.335 1.387 -0.051 1.36e-02 5.41e+03 1.43e+01 bond pdb=" CB CYS B 347 " pdb=" SG CYS B 347 " ideal model delta sigma weight residual 1.808 1.706 0.102 3.30e-02 9.18e+02 9.48e+00 bond pdb=" CG LEU A 430 " pdb=" CD2 LEU A 430 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.30e+00 bond pdb=" CB THR A 407 " pdb=" CG2 THR A 407 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" CB VAL B 42 " pdb=" CG2 VAL B 42 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.72e+00 ... (remaining 6897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 9109 2.85 - 5.70: 226 5.70 - 8.56: 26 8.56 - 11.41: 4 11.41 - 14.26: 1 Bond angle restraints: 9366 Sorted by residual: angle pdb=" C LYS B 30 " pdb=" N THR B 31 " pdb=" CA THR B 31 " ideal model delta sigma weight residual 120.69 134.95 -14.26 2.95e+00 1.15e-01 2.34e+01 angle pdb=" C ASN B 74 " pdb=" N TYR B 75 " pdb=" CA TYR B 75 " ideal model delta sigma weight residual 120.09 125.38 -5.29 1.25e+00 6.40e-01 1.79e+01 angle pdb=" C PHE B 232 " pdb=" N ASN B 233 " pdb=" CA ASN B 233 " ideal model delta sigma weight residual 122.67 117.67 5.00 1.47e+00 4.63e-01 1.16e+01 angle pdb=" CG1 ILE A 426 " pdb=" CB ILE A 426 " pdb=" CG2 ILE A 426 " ideal model delta sigma weight residual 110.70 100.76 9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA LEU A 198 " pdb=" CB LEU A 198 " pdb=" CG LEU A 198 " ideal model delta sigma weight residual 116.30 105.13 11.17 3.50e+00 8.16e-02 1.02e+01 ... (remaining 9361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 3550 16.82 - 33.63: 373 33.63 - 50.45: 72 50.45 - 67.27: 11 67.27 - 84.09: 6 Dihedral angle restraints: 4012 sinusoidal: 1524 harmonic: 2488 Sorted by residual: dihedral pdb=" CA PRO A 359 " pdb=" C PRO A 359 " pdb=" N MET A 360 " pdb=" CA MET A 360 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA LEU B 435 " pdb=" C LEU B 435 " pdb=" N ALA B 436 " pdb=" CA ALA B 436 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR B 211 " pdb=" C THR B 211 " pdb=" N LEU B 212 " pdb=" CA LEU B 212 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 668 0.049 - 0.098: 304 0.098 - 0.148: 93 0.148 - 0.197: 29 0.197 - 0.246: 8 Chirality restraints: 1102 Sorted by residual: chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILE A 288 " pdb=" CA ILE A 288 " pdb=" CG1 ILE A 288 " pdb=" CG2 ILE A 288 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 112 " pdb=" CA ILE A 112 " pdb=" CG1 ILE A 112 " pdb=" CG2 ILE A 112 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1099 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 31 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.33e+00 pdb=" N PRO A 32 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 109 " 0.051 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO B 110 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 266 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO B 267 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " 0.038 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1763 2.79 - 3.32: 6193 3.32 - 3.85: 11338 3.85 - 4.37: 13230 4.37 - 4.90: 23378 Nonbonded interactions: 55902 Sorted by model distance: nonbonded pdb=" OH TYR A 94 " pdb=" OG SER A 350 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 86 " pdb=" O GLY A 141 " model vdw 2.279 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OE1 GLU B 385 " model vdw 2.281 3.040 nonbonded pdb=" O VAL B 412 " pdb=" OG1 THR B 416 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR A 419 " pdb=" OE1 GLU B 414 " model vdw 2.313 3.040 ... (remaining 55897 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.330 Find NCS groups from input model: 0.210 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.013 0.106 6902 Z= 0.818 Angle : 1.071 14.261 9366 Z= 0.561 Chirality : 0.064 0.246 1102 Planarity : 0.009 0.076 1176 Dihedral : 14.183 84.087 2440 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.44 % Allowed : 10.47 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.11 (0.21), residues: 896 helix: -2.39 (0.14), residues: 670 sheet: None (None), residues: 0 loop : -3.15 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 124 HIS 0.007 0.002 HIS A 284 PHE 0.035 0.003 PHE A 357 TYR 0.038 0.003 TYR A 419 ARG 0.004 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.669 Fit side-chains REVERT: A 136 LEU cc_start: 0.8036 (tp) cc_final: 0.7813 (tt) REVERT: A 224 MET cc_start: 0.8224 (mmm) cc_final: 0.7959 (mmt) REVERT: B 240 ASP cc_start: 0.7938 (t0) cc_final: 0.7200 (p0) outliers start: 3 outliers final: 0 residues processed: 95 average time/residue: 0.2080 time to fit residues: 25.8506 Evaluate side-chains 76 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 20 GLN B 157 ASN B 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.103697 restraints weight = 8090.380| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.28 r_work: 0.2916 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6902 Z= 0.216 Angle : 0.537 5.718 9366 Z= 0.278 Chirality : 0.039 0.129 1102 Planarity : 0.006 0.058 1176 Dihedral : 4.437 22.038 960 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.92 % Allowed : 14.45 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.27), residues: 896 helix: -0.15 (0.19), residues: 674 sheet: None (None), residues: 0 loop : -2.90 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 124 HIS 0.002 0.001 HIS A 234 PHE 0.016 0.001 PHE B 307 TYR 0.012 0.001 TYR A 419 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.666 Fit side-chains REVERT: A 12 GLN cc_start: 0.3226 (OUTLIER) cc_final: 0.1688 (pp30) REVERT: A 360 MET cc_start: 0.8613 (mtp) cc_final: 0.8373 (mtm) REVERT: B 240 ASP cc_start: 0.8258 (t0) cc_final: 0.7314 (p0) REVERT: B 414 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8273 (mm-30) outliers start: 13 outliers final: 6 residues processed: 100 average time/residue: 0.1776 time to fit residues: 24.1777 Evaluate side-chains 87 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.127754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.104952 restraints weight = 8135.797| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.38 r_work: 0.2962 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6902 Z= 0.200 Angle : 0.508 5.653 9366 Z= 0.260 Chirality : 0.039 0.125 1102 Planarity : 0.005 0.054 1176 Dihedral : 4.125 22.672 960 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.06 % Allowed : 15.49 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.29), residues: 896 helix: 0.74 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.41 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.002 0.000 HIS A 234 PHE 0.013 0.001 PHE A 357 TYR 0.010 0.001 TYR A 419 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.677 Fit side-chains REVERT: A 12 GLN cc_start: 0.3230 (OUTLIER) cc_final: 0.0890 (pp30) REVERT: A 38 MET cc_start: 0.8341 (mmt) cc_final: 0.8094 (mmt) REVERT: A 360 MET cc_start: 0.8633 (mtp) cc_final: 0.8383 (mtm) REVERT: B 203 GLU cc_start: 0.8926 (tp30) cc_final: 0.8722 (tp30) REVERT: B 240 ASP cc_start: 0.8287 (t0) cc_final: 0.7394 (p0) outliers start: 14 outliers final: 13 residues processed: 96 average time/residue: 0.1956 time to fit residues: 25.2906 Evaluate side-chains 91 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.127716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.105221 restraints weight = 8197.612| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.38 r_work: 0.2926 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6902 Z= 0.194 Angle : 0.499 5.624 9366 Z= 0.255 Chirality : 0.039 0.125 1102 Planarity : 0.005 0.052 1176 Dihedral : 3.963 21.878 960 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.80 % Allowed : 16.52 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.29), residues: 896 helix: 1.13 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.18 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 PHE 0.022 0.001 PHE A 307 TYR 0.013 0.001 TYR A 419 ARG 0.006 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.3267 (OUTLIER) cc_final: 0.1812 (pp30) REVERT: A 360 MET cc_start: 0.8607 (mtp) cc_final: 0.8348 (mtm) REVERT: A 403 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6812 (ttp80) REVERT: B 63 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8400 (mm-40) REVERT: B 240 ASP cc_start: 0.8287 (t0) cc_final: 0.7387 (p0) outliers start: 19 outliers final: 11 residues processed: 101 average time/residue: 0.1681 time to fit residues: 23.6541 Evaluate side-chains 94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.129117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.106779 restraints weight = 8053.673| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.37 r_work: 0.2950 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6902 Z= 0.173 Angle : 0.487 5.623 9366 Z= 0.248 Chirality : 0.039 0.123 1102 Planarity : 0.004 0.050 1176 Dihedral : 3.857 21.980 960 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.95 % Allowed : 16.81 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 896 helix: 1.30 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -2.11 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 PHE 0.017 0.001 PHE A 307 TYR 0.009 0.001 TYR B 100 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.3073 (OUTLIER) cc_final: 0.1703 (pp30) REVERT: A 360 MET cc_start: 0.8619 (mtp) cc_final: 0.8370 (mtm) REVERT: A 403 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.6752 (ttp80) REVERT: B 63 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8365 (mm-40) REVERT: B 240 ASP cc_start: 0.8314 (t0) cc_final: 0.7429 (p0) REVERT: B 414 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8195 (mm-30) outliers start: 20 outliers final: 13 residues processed: 102 average time/residue: 0.1769 time to fit residues: 24.9820 Evaluate side-chains 96 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 336 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 0.0370 chunk 63 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.130393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.108119 restraints weight = 8055.952| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.38 r_work: 0.2971 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6902 Z= 0.160 Angle : 0.481 5.599 9366 Z= 0.245 Chirality : 0.038 0.122 1102 Planarity : 0.004 0.049 1176 Dihedral : 3.786 21.774 960 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.24 % Allowed : 16.96 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.30), residues: 896 helix: 1.47 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -2.01 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 PHE 0.018 0.001 PHE A 307 TYR 0.006 0.001 TYR A 419 ARG 0.006 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.3043 (OUTLIER) cc_final: 0.1798 (pp30) REVERT: A 38 MET cc_start: 0.8361 (mmt) cc_final: 0.7979 (mmt) REVERT: A 360 MET cc_start: 0.8650 (mtp) cc_final: 0.8391 (mtm) REVERT: A 403 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6749 (ttp80) REVERT: B 240 ASP cc_start: 0.8326 (t0) cc_final: 0.7444 (p0) REVERT: B 270 ASN cc_start: 0.8625 (m-40) cc_final: 0.8267 (m-40) REVERT: B 304 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7726 (mp) REVERT: B 425 MET cc_start: 0.8997 (mtt) cc_final: 0.8748 (mtp) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.1575 time to fit residues: 22.8976 Evaluate side-chains 98 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.0570 chunk 77 optimal weight: 0.7980 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.128893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106662 restraints weight = 8076.598| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.37 r_work: 0.2963 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6902 Z= 0.193 Angle : 0.501 7.061 9366 Z= 0.252 Chirality : 0.039 0.121 1102 Planarity : 0.004 0.048 1176 Dihedral : 3.765 21.545 960 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.83 % Allowed : 16.67 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.29), residues: 896 helix: 1.50 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -1.97 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 PHE 0.018 0.001 PHE A 307 TYR 0.009 0.001 TYR B 100 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.3171 (OUTLIER) cc_final: 0.1866 (pp30) REVERT: A 38 MET cc_start: 0.8431 (mmt) cc_final: 0.7853 (mmt) REVERT: A 103 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: A 111 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 360 MET cc_start: 0.8688 (mtp) cc_final: 0.8432 (mtm) REVERT: A 403 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6770 (ttp80) REVERT: B 240 ASP cc_start: 0.8310 (t0) cc_final: 0.7487 (p0) outliers start: 26 outliers final: 18 residues processed: 102 average time/residue: 0.1620 time to fit residues: 23.3440 Evaluate side-chains 99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 0.0020 chunk 24 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 79 optimal weight: 0.0060 chunk 30 optimal weight: 0.9980 overall best weight: 0.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.132572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.110472 restraints weight = 8020.205| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.37 r_work: 0.2997 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6902 Z= 0.148 Angle : 0.486 8.892 9366 Z= 0.242 Chirality : 0.038 0.128 1102 Planarity : 0.004 0.048 1176 Dihedral : 3.669 21.765 960 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.80 % Allowed : 17.85 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.34 (0.30), residues: 896 helix: 1.67 (0.21), residues: 688 sheet: None (None), residues: 0 loop : -1.82 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 PHE 0.019 0.001 PHE A 307 TYR 0.005 0.001 TYR A 445 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.672 Fit side-chains REVERT: A 12 GLN cc_start: 0.2979 (OUTLIER) cc_final: 0.1909 (pp30) REVERT: A 38 MET cc_start: 0.8409 (mmt) cc_final: 0.7988 (mmt) REVERT: A 103 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7703 (pp20) REVERT: A 111 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 360 MET cc_start: 0.8649 (mtp) cc_final: 0.8420 (mtm) REVERT: B 240 ASP cc_start: 0.8302 (t0) cc_final: 0.7433 (p0) REVERT: B 455 LYS cc_start: 0.8060 (tttt) cc_final: 0.7806 (ttmm) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 0.1713 time to fit residues: 24.9741 Evaluate side-chains 96 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 0.0060 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.131533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.109100 restraints weight = 8189.593| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.38 r_work: 0.3038 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6902 Z= 0.173 Angle : 0.510 8.950 9366 Z= 0.252 Chirality : 0.039 0.122 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.652 21.634 960 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.65 % Allowed : 17.85 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.30), residues: 896 helix: 1.75 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 PHE 0.019 0.001 PHE A 307 TYR 0.014 0.001 TYR B 100 ARG 0.004 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.665 Fit side-chains REVERT: A 12 GLN cc_start: 0.3005 (OUTLIER) cc_final: 0.1898 (pp30) REVERT: A 38 MET cc_start: 0.8445 (mmt) cc_final: 0.8053 (mmt) REVERT: A 103 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7679 (pp20) REVERT: A 111 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7546 (tm-30) REVERT: A 415 MET cc_start: 0.7837 (ptp) cc_final: 0.7496 (ptp) REVERT: B 143 MET cc_start: 0.8695 (mtp) cc_final: 0.8420 (mtt) REVERT: B 161 MET cc_start: 0.7972 (ttp) cc_final: 0.7538 (ptm) REVERT: B 240 ASP cc_start: 0.8238 (t0) cc_final: 0.7405 (p0) outliers start: 18 outliers final: 14 residues processed: 101 average time/residue: 0.1505 time to fit residues: 22.0724 Evaluate side-chains 100 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.0040 chunk 81 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.131579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.109211 restraints weight = 8182.539| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.38 r_work: 0.3042 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6902 Z= 0.172 Angle : 0.510 9.104 9366 Z= 0.252 Chirality : 0.039 0.122 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.648 21.968 960 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.36 % Allowed : 18.29 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.48 (0.30), residues: 896 helix: 1.80 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -1.79 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 59 HIS 0.004 0.000 HIS A 234 PHE 0.020 0.001 PHE A 307 TYR 0.006 0.001 TYR B 419 ARG 0.004 0.000 ARG B 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.740 Fit side-chains REVERT: A 12 GLN cc_start: 0.2950 (OUTLIER) cc_final: 0.1857 (pp30) REVERT: A 38 MET cc_start: 0.8473 (mmt) cc_final: 0.8082 (mmt) REVERT: A 103 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7655 (pp20) REVERT: A 111 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 240 ASP cc_start: 0.8268 (t0) cc_final: 0.7443 (p0) outliers start: 16 outliers final: 13 residues processed: 97 average time/residue: 0.1510 time to fit residues: 21.2915 Evaluate side-chains 98 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.126361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.103690 restraints weight = 8246.198| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.38 r_work: 0.2955 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6902 Z= 0.276 Angle : 0.567 8.630 9366 Z= 0.281 Chirality : 0.042 0.201 1102 Planarity : 0.005 0.046 1176 Dihedral : 3.860 23.977 960 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 18.29 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.29), residues: 896 helix: 1.59 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -1.76 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 59 HIS 0.004 0.001 HIS A 234 PHE 0.020 0.002 PHE A 307 TYR 0.024 0.002 TYR B 100 ARG 0.004 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3139.76 seconds wall clock time: 54 minutes 32.73 seconds (3272.73 seconds total)