Starting phenix.real_space_refine on Tue Mar 3 15:34:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rnx_24582/03_2026/7rnx_24582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rnx_24582/03_2026/7rnx_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rnx_24582/03_2026/7rnx_24582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rnx_24582/03_2026/7rnx_24582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rnx_24582/03_2026/7rnx_24582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rnx_24582/03_2026/7rnx_24582.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.54, per 1000 atoms: 0.23 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: 0.62 Conformation dependent library (CDL) restraints added in 212.8 milliseconds 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: 0.18 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: 0.90 Time building geometry restraints manager: 0.78 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: 0.01 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: 0.570 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: 0.090 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.480 ------------------------------------------------------------------------------- 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= 0.487 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.004 0.001 ARG B 120 TYR 0.038 0.003 TYR A 419 PHE 0.035 0.003 PHE A 357 TRP 0.020 0.003 TRP B 124 HIS 0.007 0.002 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.01255 ( 6902) covalent geometry : angle 1.07066 ( 9366) hydrogen bonds : bond 0.08748 ( 477) hydrogen bonds : angle 5.87897 ( 1425) *********************** 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 : 0.174 Fit side-chains REVERT: A 136 LEU cc_start: 0.8036 (tp) cc_final: 0.7813 (tt) REVERT: A 224 MET cc_start: 0.8225 (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: 0.0881 time to fit residues: 10.9600 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.124565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.103225 restraints weight = 8281.012| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.30 r_work: 0.2910 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6902 Z= 0.147 Angle : 0.548 5.750 9366 Z= 0.283 Chirality : 0.040 0.129 1102 Planarity : 0.006 0.058 1176 Dihedral : 4.485 22.355 960 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.92 % Allowed : 14.31 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.26), residues: 896 helix: -0.23 (0.19), residues: 674 sheet: None (None), residues: 0 loop : -2.91 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.013 0.001 TYR A 419 PHE 0.016 0.001 PHE B 307 TRP 0.012 0.001 TRP B 124 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6902) covalent geometry : angle 0.54846 ( 9366) hydrogen bonds : bond 0.04021 ( 477) hydrogen bonds : angle 4.57308 ( 1425) *********************** 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 102 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.227 Fit side-chains REVERT: A 12 GLN cc_start: 0.3230 (OUTLIER) cc_final: 0.1689 (pp30) REVERT: A 360 MET cc_start: 0.8627 (mtp) cc_final: 0.8401 (mtm) REVERT: B 240 ASP cc_start: 0.8254 (t0) cc_final: 0.7324 (p0) REVERT: B 414 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8276 (mm-30) outliers start: 13 outliers final: 6 residues processed: 99 average time/residue: 0.0821 time to fit residues: 11.0925 Evaluate side-chains 86 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.127277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.104631 restraints weight = 8098.336| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.37 r_work: 0.2920 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1512 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= 0.132 Angle : 0.510 5.667 9366 Z= 0.262 Chirality : 0.039 0.125 1102 Planarity : 0.005 0.054 1176 Dihedral : 4.136 22.591 960 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.21 % Allowed : 15.19 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.29), residues: 896 helix: 0.72 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.40 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.011 0.001 TYR B 419 PHE 0.013 0.001 PHE A 357 TRP 0.010 0.001 TRP B 124 HIS 0.002 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6902) covalent geometry : angle 0.51023 ( 9366) hydrogen bonds : bond 0.03668 ( 477) hydrogen bonds : angle 4.26535 ( 1425) *********************** 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 98 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.242 Fit side-chains REVERT: A 12 GLN cc_start: 0.3206 (OUTLIER) cc_final: 0.0907 (pp30) REVERT: A 38 MET cc_start: 0.8349 (mmt) cc_final: 0.8067 (mmt) REVERT: A 360 MET cc_start: 0.8616 (mtp) cc_final: 0.8379 (mtm) REVERT: B 203 GLU cc_start: 0.8932 (tp30) cc_final: 0.8709 (tp30) REVERT: B 240 ASP cc_start: 0.8331 (t0) cc_final: 0.7375 (p0) outliers start: 15 outliers final: 13 residues processed: 95 average time/residue: 0.0849 time to fit residues: 11.0060 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 : 0.250 ------------------------------------------------------------------------------- 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 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.128409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.106077 restraints weight = 8168.600| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.37 r_work: 0.2941 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6902 Z= 0.114 Angle : 0.489 5.626 9366 Z= 0.250 Chirality : 0.038 0.125 1102 Planarity : 0.005 0.052 1176 Dihedral : 3.944 21.946 960 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 16.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.29), residues: 896 helix: 1.16 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.17 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.011 0.001 TYR A 419 PHE 0.022 0.001 PHE A 307 TRP 0.014 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6902) covalent geometry : angle 0.48936 ( 9366) hydrogen bonds : bond 0.03418 ( 477) hydrogen bonds : angle 4.09896 ( 1425) *********************** 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 105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.3220 (OUTLIER) cc_final: 0.1784 (pp30) REVERT: A 360 MET cc_start: 0.8593 (mtp) cc_final: 0.8341 (mtm) REVERT: A 403 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.6764 (ttp80) REVERT: B 240 ASP cc_start: 0.8235 (t0) cc_final: 0.7323 (p0) outliers start: 17 outliers final: 10 residues processed: 102 average time/residue: 0.0756 time to fit residues: 10.6809 Evaluate side-chains 90 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 403 ARG Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.0000 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.129182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.106680 restraints weight = 8145.810| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.38 r_work: 0.2940 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6902 Z= 0.116 Angle : 0.490 5.603 9366 Z= 0.249 Chirality : 0.039 0.123 1102 Planarity : 0.004 0.050 1176 Dihedral : 3.850 21.942 960 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.10 % Allowed : 16.52 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.29), residues: 896 helix: 1.26 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -2.12 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.008 0.001 TYR A 419 PHE 0.017 0.001 PHE A 307 TRP 0.017 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6902) covalent geometry : angle 0.48975 ( 9366) hydrogen bonds : bond 0.03402 ( 477) hydrogen bonds : angle 4.01730 ( 1425) *********************** 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 105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.3099 (OUTLIER) cc_final: 0.1726 (pp30) REVERT: A 360 MET cc_start: 0.8637 (mtp) cc_final: 0.8404 (mtm) REVERT: A 403 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.6763 (ttp80) REVERT: B 240 ASP cc_start: 0.8252 (t0) cc_final: 0.7309 (p0) outliers start: 21 outliers final: 13 residues processed: 101 average time/residue: 0.0604 time to fit residues: 8.6962 Evaluate side-chains 95 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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 336 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 56 optimal weight: 0.0040 chunk 80 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.129418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.106944 restraints weight = 8150.366| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.39 r_work: 0.2948 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6902 Z= 0.116 Angle : 0.489 5.598 9366 Z= 0.249 Chirality : 0.039 0.123 1102 Planarity : 0.004 0.049 1176 Dihedral : 3.807 21.521 960 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.95 % Allowed : 16.67 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.29), residues: 896 helix: 1.40 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -1.98 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.009 0.001 TYR B 100 PHE 0.014 0.001 PHE A 307 TRP 0.017 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6902) covalent geometry : angle 0.48920 ( 9366) hydrogen bonds : bond 0.03367 ( 477) hydrogen bonds : angle 3.95420 ( 1425) *********************** 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 102 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.2989 (OUTLIER) cc_final: 0.1722 (pp30) REVERT: A 38 MET cc_start: 0.8360 (mmt) cc_final: 0.7974 (mmt) REVERT: A 360 MET cc_start: 0.8635 (mtp) cc_final: 0.8408 (mtm) REVERT: A 403 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6798 (ttp80) REVERT: B 240 ASP cc_start: 0.8273 (t0) cc_final: 0.7351 (p0) outliers start: 20 outliers final: 16 residues processed: 97 average time/residue: 0.0700 time to fit residues: 9.6253 Evaluate side-chains 97 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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 A residue 415 MET Chi-restraints excluded: chain B residue 122 VAL 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 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 88 optimal weight: 0.0370 chunk 22 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.131514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.109102 restraints weight = 7990.524| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.38 r_work: 0.2975 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2186 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= 0.104 Angle : 0.485 7.221 9366 Z= 0.245 Chirality : 0.038 0.120 1102 Planarity : 0.004 0.048 1176 Dihedral : 3.743 21.803 960 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.80 % Allowed : 17.26 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.30), residues: 896 helix: 1.57 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -1.94 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.006 0.001 TYR B 419 PHE 0.019 0.001 PHE A 307 TRP 0.016 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 6902) covalent geometry : angle 0.48489 ( 9366) hydrogen bonds : bond 0.03181 ( 477) hydrogen bonds : angle 3.85478 ( 1425) *********************** 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 105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.232 Fit side-chains REVERT: A 12 GLN cc_start: 0.3064 (OUTLIER) cc_final: 0.1886 (pp30) REVERT: A 38 MET cc_start: 0.8411 (mmt) cc_final: 0.7780 (mmt) REVERT: A 103 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: A 360 MET cc_start: 0.8651 (mtp) cc_final: 0.8409 (mtm) REVERT: B 240 ASP cc_start: 0.8236 (t0) cc_final: 0.7360 (p0) REVERT: B 270 ASN cc_start: 0.8624 (m-40) cc_final: 0.8254 (m-40) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.0662 time to fit residues: 9.6773 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 : 0.230 ------------------------------------------------------------------------------- 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 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL 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 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 80 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 74 ASN A 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.129598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.106957 restraints weight = 8163.820| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.39 r_work: 0.2946 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2155 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= 0.124 Angle : 0.514 8.679 9366 Z= 0.257 Chirality : 0.039 0.122 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.745 21.344 960 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.10 % Allowed : 17.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.29), residues: 896 helix: 1.57 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -1.91 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.010 0.001 TYR B 100 PHE 0.019 0.001 PHE A 307 TRP 0.017 0.001 TRP A 59 HIS 0.002 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6902) covalent geometry : angle 0.51425 ( 9366) hydrogen bonds : bond 0.03376 ( 477) hydrogen bonds : angle 3.90617 ( 1425) *********************** 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 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.192 Fit side-chains REVERT: A 12 GLN cc_start: 0.3079 (OUTLIER) cc_final: 0.1881 (pp30) REVERT: A 38 MET cc_start: 0.8469 (mmt) cc_final: 0.8015 (mmt) REVERT: A 103 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7697 (pp20) REVERT: A 111 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 360 MET cc_start: 0.8676 (mtp) cc_final: 0.8426 (mtm) REVERT: B 240 ASP cc_start: 0.8334 (t0) cc_final: 0.7450 (p0) outliers start: 21 outliers final: 16 residues processed: 105 average time/residue: 0.0584 time to fit residues: 9.0628 Evaluate side-chains 101 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3335 r_free = 0.3335 target = 0.129022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.106448 restraints weight = 8127.698| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.38 r_work: 0.2938 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6902 Z= 0.136 Angle : 0.528 8.772 9366 Z= 0.264 Chirality : 0.040 0.123 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.785 21.384 960 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.10 % Allowed : 17.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 896 helix: 1.57 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -1.89 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.009 0.001 TYR A 419 PHE 0.020 0.001 PHE A 307 TRP 0.018 0.001 TRP A 59 HIS 0.001 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6902) covalent geometry : angle 0.52844 ( 9366) hydrogen bonds : bond 0.03489 ( 477) hydrogen bonds : angle 3.92836 ( 1425) *********************** 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: 21 poor density : 82 time to evaluate : 0.271 Fit side-chains REVERT: A 12 GLN cc_start: 0.3098 (OUTLIER) cc_final: 0.1893 (pp30) REVERT: A 103 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7687 (pp20) REVERT: A 111 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 360 MET cc_start: 0.8675 (mtp) cc_final: 0.8432 (mtm) REVERT: B 99 LYS cc_start: 0.8418 (tppt) cc_final: 0.8216 (tptm) REVERT: B 240 ASP cc_start: 0.8306 (t0) cc_final: 0.7447 (p0) outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 0.0621 time to fit residues: 9.0429 Evaluate side-chains 100 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 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 A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.0270 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.132099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.109565 restraints weight = 8078.501| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.38 r_work: 0.2975 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6902 Z= 0.109 Angle : 0.505 8.800 9366 Z= 0.253 Chirality : 0.039 0.122 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.699 21.461 960 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.95 % Allowed : 17.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.30), residues: 896 helix: 1.69 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -1.82 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.011 0.001 TYR B 100 PHE 0.020 0.001 PHE A 307 TRP 0.015 0.001 TRP A 59 HIS 0.001 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6902) covalent geometry : angle 0.50511 ( 9366) hydrogen bonds : bond 0.03274 ( 477) hydrogen bonds : angle 3.84248 ( 1425) ********************** 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 105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.233 Fit side-chains REVERT: A 12 GLN cc_start: 0.3031 (OUTLIER) cc_final: 0.1852 (pp30) REVERT: A 103 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.7668 (pp20) REVERT: A 111 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7578 (tm-30) REVERT: B 161 MET cc_start: 0.7982 (ttp) cc_final: 0.7458 (ptm) REVERT: B 240 ASP cc_start: 0.8302 (t0) cc_final: 0.7449 (p0) REVERT: B 270 ASN cc_start: 0.8645 (m-40) cc_final: 0.8273 (m-40) outliers start: 20 outliers final: 17 residues processed: 102 average time/residue: 0.0657 time to fit residues: 9.6731 Evaluate side-chains 101 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain A residue 318 ASN 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 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 41 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.130490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.107798 restraints weight = 8057.321| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.38 r_work: 0.2993 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6902 Z= 0.121 Angle : 0.531 9.492 9366 Z= 0.262 Chirality : 0.040 0.122 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.707 22.123 960 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.24 % Allowed : 17.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.30), residues: 896 helix: 1.70 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -1.79 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.007 0.001 TYR B 419 PHE 0.020 0.001 PHE A 307 TRP 0.016 0.001 TRP A 59 HIS 0.001 0.000 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6902) covalent geometry : angle 0.53075 ( 9366) hydrogen bonds : bond 0.03347 ( 477) hydrogen bonds : angle 3.84779 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1473.28 seconds wall clock time: 25 minutes 53.31 seconds (1553.31 seconds total)