Starting phenix.real_space_refine on Thu Sep 26 02:12:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/09_2024/8x82_38133_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/09_2024/8x82_38133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/09_2024/8x82_38133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/09_2024/8x82_38133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/09_2024/8x82_38133_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/09_2024/8x82_38133_neut.cif" } resolution = 2.8 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= 0.000 sd= 0.006 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 72 5.16 5 C 7796 2.51 5 N 2048 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12004 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3001 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 6.17, per 1000 atoms: 0.51 Number of scatterers: 12004 At special positions: 0 Unit cell: (108.81, 108.81, 105.09, 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 72 16.00 O 2088 8.00 N 2048 7.00 C 7796 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: 3.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 85.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN A 123 " --> pdb=" O ASN A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 124 through 162 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 357 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.651A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'B' and resid 37 through 64 Processing helix chain 'B' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN B 123 " --> pdb=" O ASN B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 124 through 162 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 357 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.652A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 37 through 64 Processing helix chain 'C' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN C 123 " --> pdb=" O ASN C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 124 through 162 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 357 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.651A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 37 through 64 Processing helix chain 'D' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN D 123 " --> pdb=" O ASN D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 124 through 162 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 357 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 357 through 369 Processing helix chain 'D' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.651A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL A 25 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL B 25 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL C 25 " --> pdb=" O GLU C 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL D 25 " --> pdb=" O GLU D 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3204 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: 3.68 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3790 1.34 - 1.46: 2718 1.46 - 1.58: 5616 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 12236 Sorted by residual: bond pdb=" CA ILE A 176 " pdb=" C ILE A 176 " ideal model delta sigma weight residual 1.520 1.528 -0.009 8.80e-03 1.29e+04 9.99e-01 bond pdb=" CA ILE B 176 " pdb=" C ILE B 176 " ideal model delta sigma weight residual 1.520 1.528 -0.009 8.80e-03 1.29e+04 9.99e-01 bond pdb=" C ILE B 67 " pdb=" O ILE B 67 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.92e-01 bond pdb=" C ILE D 67 " pdb=" O ILE D 67 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.92e-01 bond pdb=" C ILE D 176 " pdb=" N PRO D 177 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.36e-01 ... (remaining 12231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 16165 1.00 - 2.00: 338 2.00 - 3.01: 63 3.01 - 4.01: 18 4.01 - 5.01: 12 Bond angle restraints: 16596 Sorted by residual: angle pdb=" C TYR B 175 " pdb=" N ILE B 176 " pdb=" CA ILE B 176 " ideal model delta sigma weight residual 120.24 123.00 -2.76 6.30e-01 2.52e+00 1.91e+01 angle pdb=" C TYR A 175 " pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 120.24 123.00 -2.76 6.30e-01 2.52e+00 1.91e+01 angle pdb=" C TYR C 175 " pdb=" N ILE C 176 " pdb=" CA ILE C 176 " ideal model delta sigma weight residual 120.33 123.03 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" C TYR D 175 " pdb=" N ILE D 176 " pdb=" CA ILE D 176 " ideal model delta sigma weight residual 120.33 123.03 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" C VAL D 345 " pdb=" N GLU D 346 " pdb=" CA GLU D 346 " ideal model delta sigma weight residual 120.26 124.12 -3.86 1.34e+00 5.57e-01 8.31e+00 ... (remaining 16591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 6284 17.10 - 34.21: 712 34.21 - 51.31: 200 51.31 - 68.42: 32 68.42 - 85.52: 24 Dihedral angle restraints: 7252 sinusoidal: 2792 harmonic: 4460 Sorted by residual: dihedral pdb=" CA ASP B 276 " pdb=" CB ASP B 276 " pdb=" CG ASP B 276 " pdb=" OD1 ASP B 276 " ideal model delta sinusoidal sigma weight residual -30.00 -88.04 58.04 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP D 276 " pdb=" CB ASP D 276 " pdb=" CG ASP D 276 " pdb=" OD1 ASP D 276 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 276 " pdb=" CB ASP A 276 " pdb=" CG ASP A 276 " pdb=" OD1 ASP A 276 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 7249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1210 0.024 - 0.047: 470 0.047 - 0.071: 244 0.071 - 0.095: 37 0.095 - 0.119: 27 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE D 163 " pdb=" N ILE D 163 " pdb=" C ILE D 163 " pdb=" CB ILE D 163 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 1985 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 176 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO B 177 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 176 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO A 177 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 176 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO C 177 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 177 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 177 " -0.014 5.00e-02 4.00e+02 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 284 2.72 - 3.27: 12504 3.27 - 3.81: 21460 3.81 - 4.36: 23941 4.36 - 4.90: 42851 Nonbonded interactions: 101040 Sorted by model distance: nonbonded pdb=" O ALA D 81 " pdb=" OG SER D 85 " model vdw 2.181 3.040 nonbonded pdb=" O ALA A 81 " pdb=" OG SER A 85 " model vdw 2.181 3.040 nonbonded pdb=" O ALA C 81 " pdb=" OG SER C 85 " model vdw 2.181 3.040 nonbonded pdb=" O ALA B 81 " pdb=" OG SER B 85 " model vdw 2.181 3.040 nonbonded pdb=" OD1 ASN A 207 " pdb=" OG1 THR A 358 " model vdw 2.244 3.040 ... (remaining 101035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.680 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.670 Find NCS groups from input model: 0.370 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12236 Z= 0.134 Angle : 0.408 5.012 16596 Z= 0.260 Chirality : 0.033 0.119 1988 Planarity : 0.002 0.025 2032 Dihedral : 16.428 85.523 4356 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.84 % Allowed : 18.12 % Favored : 81.04 % 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: 3.68 (0.21), residues: 1504 helix: 3.02 (0.13), residues: 1248 sheet: 1.67 (0.77), residues: 48 loop : -1.49 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 154 HIS 0.002 0.001 HIS A 306 PHE 0.007 0.001 PHE B 178 TYR 0.005 0.001 TYR B 415 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.239 Fit side-chains REVERT: A 126 ARG cc_start: 0.6565 (mmm160) cc_final: 0.5840 (mtm110) REVERT: A 129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7061 (ttm170) REVERT: A 131 ARG cc_start: 0.6936 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: A 272 LYS cc_start: 0.6744 (tppp) cc_final: 0.5990 (ttpp) REVERT: A 279 GLU cc_start: 0.8121 (tt0) cc_final: 0.7790 (tt0) REVERT: A 367 ARG cc_start: 0.6379 (mtm-85) cc_final: 0.6145 (mtm-85) REVERT: A 399 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7120 (tpt170) REVERT: B 126 ARG cc_start: 0.6536 (mmm160) cc_final: 0.5802 (mtm110) REVERT: B 129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7064 (ttm170) REVERT: B 131 ARG cc_start: 0.6936 (mpt-90) cc_final: 0.5481 (tmt-80) REVERT: B 272 LYS cc_start: 0.6761 (tppp) cc_final: 0.5993 (ttpp) REVERT: B 279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7791 (tt0) REVERT: B 399 ARG cc_start: 0.7769 (mtm180) cc_final: 0.7140 (tpt170) REVERT: C 126 ARG cc_start: 0.6535 (mmm160) cc_final: 0.5800 (mtm110) REVERT: C 129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7064 (ttm170) REVERT: C 131 ARG cc_start: 0.6938 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: C 272 LYS cc_start: 0.6743 (tppp) cc_final: 0.5988 (ttpp) REVERT: C 279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7791 (tt0) REVERT: C 399 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7175 (tpt170) REVERT: D 126 ARG cc_start: 0.6563 (mmm160) cc_final: 0.5840 (mtm110) REVERT: D 129 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.7061 (ttm170) REVERT: D 131 ARG cc_start: 0.6938 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: D 272 LYS cc_start: 0.6744 (tppp) cc_final: 0.5985 (ttpp) REVERT: D 279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7716 (tt0) REVERT: D 399 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7137 (tpt170) outliers start: 11 outliers final: 0 residues processed: 191 average time/residue: 1.2409 time to fit residues: 254.8629 Evaluate side-chains 136 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 383 GLN A 421 GLN A 423 GLN B 189 GLN B 383 GLN B 421 GLN B 423 GLN C 189 GLN C 383 GLN C 421 GLN C 423 GLN D 189 GLN D 383 GLN D 421 GLN D 423 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12236 Z= 0.311 Angle : 0.507 4.881 16596 Z= 0.276 Chirality : 0.039 0.133 1988 Planarity : 0.004 0.025 2032 Dihedral : 3.548 12.475 1656 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.06 % Allowed : 15.60 % Favored : 81.35 % 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: 3.11 (0.20), residues: 1504 helix: 2.56 (0.13), residues: 1260 sheet: 1.23 (0.76), residues: 48 loop : -1.33 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 130 HIS 0.003 0.001 HIS B 349 PHE 0.013 0.002 PHE C 11 TYR 0.017 0.002 TYR B 175 ARG 0.003 0.001 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 1.257 Fit side-chains REVERT: A 33 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 51 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7522 (mmt) REVERT: A 114 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6753 (mtmt) REVERT: A 126 ARG cc_start: 0.6415 (mtm110) cc_final: 0.5671 (mtm110) REVERT: A 131 ARG cc_start: 0.6982 (mpt-90) cc_final: 0.5450 (tmt-80) REVERT: A 272 LYS cc_start: 0.7042 (tppp) cc_final: 0.6389 (ttpp) REVERT: A 279 GLU cc_start: 0.8136 (tt0) cc_final: 0.7792 (tt0) REVERT: A 290 ASN cc_start: 0.8615 (t0) cc_final: 0.8367 (t0) REVERT: A 399 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7211 (tpt170) REVERT: B 33 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7288 (mt-10) REVERT: B 51 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7522 (mmt) REVERT: B 114 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6751 (mtmt) REVERT: B 126 ARG cc_start: 0.6414 (mtm110) cc_final: 0.5672 (mtm110) REVERT: B 131 ARG cc_start: 0.6983 (mpt-90) cc_final: 0.5450 (tmt-80) REVERT: B 272 LYS cc_start: 0.7056 (tppp) cc_final: 0.6389 (ttpp) REVERT: B 279 GLU cc_start: 0.8114 (tt0) cc_final: 0.7767 (tt0) REVERT: B 290 ASN cc_start: 0.8614 (t0) cc_final: 0.8365 (t0) REVERT: B 399 ARG cc_start: 0.7964 (mtm180) cc_final: 0.7219 (tpt170) REVERT: C 51 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7526 (mmt) REVERT: C 114 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6752 (mtmt) REVERT: C 126 ARG cc_start: 0.6412 (mtm110) cc_final: 0.5695 (mtm110) REVERT: C 131 ARG cc_start: 0.6984 (mpt-90) cc_final: 0.5451 (tmt-80) REVERT: C 272 LYS cc_start: 0.7038 (tppp) cc_final: 0.6386 (ttpp) REVERT: C 279 GLU cc_start: 0.8133 (tt0) cc_final: 0.7790 (tt0) REVERT: C 290 ASN cc_start: 0.8614 (t0) cc_final: 0.8365 (t0) REVERT: C 399 ARG cc_start: 0.7965 (mtm180) cc_final: 0.7219 (tpt170) REVERT: D 33 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7290 (mt-10) REVERT: D 51 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7527 (mmt) REVERT: D 114 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6752 (mtmt) REVERT: D 126 ARG cc_start: 0.6414 (mtm110) cc_final: 0.5671 (mtm110) REVERT: D 131 ARG cc_start: 0.6986 (mpt-90) cc_final: 0.5452 (tmt-80) REVERT: D 272 LYS cc_start: 0.7037 (tppp) cc_final: 0.6383 (ttpp) REVERT: D 279 GLU cc_start: 0.8163 (tt0) cc_final: 0.7893 (tt0) REVERT: D 290 ASN cc_start: 0.8615 (t0) cc_final: 0.8367 (t0) REVERT: D 399 ARG cc_start: 0.7981 (mtm180) cc_final: 0.7257 (tpt170) outliers start: 40 outliers final: 12 residues processed: 172 average time/residue: 1.3060 time to fit residues: 241.7734 Evaluate side-chains 172 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 383 GLN B 189 GLN B 383 GLN C 27 ASN C 189 GLN C 383 GLN D 189 GLN D 383 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12236 Z= 0.201 Angle : 0.426 4.965 16596 Z= 0.236 Chirality : 0.036 0.130 1988 Planarity : 0.003 0.027 2032 Dihedral : 3.493 12.720 1656 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.22 % Allowed : 17.20 % Favored : 80.58 % 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: 3.23 (0.21), residues: 1504 helix: 2.64 (0.13), residues: 1264 sheet: 1.23 (0.72), residues: 48 loop : -1.34 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.002 0.001 HIS A 349 PHE 0.012 0.002 PHE D 422 TYR 0.009 0.001 TYR B 175 ARG 0.003 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.354 Fit side-chains REVERT: A 25 VAL cc_start: 0.7946 (p) cc_final: 0.7701 (m) REVERT: A 33 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7197 (mt-10) REVERT: A 126 ARG cc_start: 0.6384 (mtm110) cc_final: 0.5662 (mtm110) REVERT: A 131 ARG cc_start: 0.7000 (mpt-90) cc_final: 0.5445 (tmt-80) REVERT: A 173 HIS cc_start: 0.6226 (OUTLIER) cc_final: 0.5335 (m-70) REVERT: A 272 LYS cc_start: 0.7053 (tppp) cc_final: 0.6491 (ttpp) REVERT: A 279 GLU cc_start: 0.8103 (tt0) cc_final: 0.7691 (tt0) REVERT: A 290 ASN cc_start: 0.8582 (t0) cc_final: 0.8274 (t0) REVERT: A 313 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.6064 (m-10) REVERT: A 331 MET cc_start: 0.6579 (ttp) cc_final: 0.6282 (ttp) REVERT: A 364 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6735 (mm-30) REVERT: A 399 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7235 (tpt170) REVERT: B 25 VAL cc_start: 0.7944 (p) cc_final: 0.7698 (m) REVERT: B 33 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7191 (mt-10) REVERT: B 126 ARG cc_start: 0.6380 (mtm110) cc_final: 0.5659 (mtm110) REVERT: B 131 ARG cc_start: 0.7001 (mpt-90) cc_final: 0.5446 (tmt-80) REVERT: B 272 LYS cc_start: 0.7080 (tppp) cc_final: 0.6497 (ttpp) REVERT: B 279 GLU cc_start: 0.8101 (tt0) cc_final: 0.7689 (tt0) REVERT: B 290 ASN cc_start: 0.8583 (t0) cc_final: 0.8273 (t0) REVERT: B 313 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6059 (m-10) REVERT: B 331 MET cc_start: 0.6572 (ttp) cc_final: 0.6291 (ttp) REVERT: B 364 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6728 (mm-30) REVERT: B 399 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7246 (tpt170) REVERT: C 25 VAL cc_start: 0.7850 (p) cc_final: 0.7636 (m) REVERT: C 126 ARG cc_start: 0.6383 (mtm110) cc_final: 0.5668 (mtm110) REVERT: C 131 ARG cc_start: 0.7002 (mpt-90) cc_final: 0.5447 (tmt-80) REVERT: C 272 LYS cc_start: 0.7057 (tppp) cc_final: 0.6498 (ttpp) REVERT: C 279 GLU cc_start: 0.8100 (tt0) cc_final: 0.7687 (tt0) REVERT: C 290 ASN cc_start: 0.8584 (t0) cc_final: 0.8272 (t0) REVERT: C 313 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.5994 (m-10) REVERT: C 331 MET cc_start: 0.6573 (ttp) cc_final: 0.6291 (ttp) REVERT: C 364 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6730 (mm-30) REVERT: C 399 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7245 (tpt170) REVERT: D 25 VAL cc_start: 0.7946 (p) cc_final: 0.7702 (m) REVERT: D 33 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7201 (mt-10) REVERT: D 126 ARG cc_start: 0.6382 (mtm110) cc_final: 0.5661 (mtm110) REVERT: D 131 ARG cc_start: 0.7005 (mpt-90) cc_final: 0.5447 (tmt-80) REVERT: D 272 LYS cc_start: 0.7073 (tppp) cc_final: 0.6496 (ttpp) REVERT: D 279 GLU cc_start: 0.8064 (tt0) cc_final: 0.7739 (tt0) REVERT: D 290 ASN cc_start: 0.8584 (t0) cc_final: 0.8274 (t0) REVERT: D 313 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.6053 (m-10) REVERT: D 331 MET cc_start: 0.6576 (ttp) cc_final: 0.6280 (ttp) REVERT: D 364 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6728 (mm-30) REVERT: D 399 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7246 (tpt170) outliers start: 29 outliers final: 12 residues processed: 181 average time/residue: 1.2432 time to fit residues: 245.2163 Evaluate side-chains 179 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 313 PHE Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12236 Z= 0.326 Angle : 0.504 5.714 16596 Z= 0.274 Chirality : 0.039 0.130 1988 Planarity : 0.003 0.024 2032 Dihedral : 3.681 12.602 1656 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.21 % Allowed : 15.67 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.79 (0.20), residues: 1504 helix: 2.35 (0.13), residues: 1264 sheet: 1.22 (0.68), residues: 48 loop : -1.56 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 174 HIS 0.003 0.001 HIS C 337 PHE 0.013 0.002 PHE D 422 TYR 0.014 0.002 TYR B 175 ARG 0.004 0.001 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 1.440 Fit side-chains REVERT: A 25 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7603 (m) REVERT: A 33 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 71 MET cc_start: 0.6777 (mmm) cc_final: 0.6203 (mmm) REVERT: A 114 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6705 (mtmt) REVERT: A 126 ARG cc_start: 0.6472 (mtm110) cc_final: 0.5747 (mtm110) REVERT: A 131 ARG cc_start: 0.7043 (mpt-90) cc_final: 0.5474 (ttt180) REVERT: A 155 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5967 (mtp) REVERT: A 272 LYS cc_start: 0.7006 (tppp) cc_final: 0.6420 (ttpp) REVERT: A 279 GLU cc_start: 0.8146 (tt0) cc_final: 0.7776 (tt0) REVERT: A 331 MET cc_start: 0.6541 (ttp) cc_final: 0.6270 (ttp) REVERT: A 380 LYS cc_start: 0.7047 (mmtp) cc_final: 0.6569 (mmmt) REVERT: A 399 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7261 (tpt170) REVERT: B 25 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7603 (m) REVERT: B 33 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 71 MET cc_start: 0.6774 (mmm) cc_final: 0.6201 (mmm) REVERT: B 114 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6706 (mtmt) REVERT: B 126 ARG cc_start: 0.6471 (mtm110) cc_final: 0.5756 (mtm110) REVERT: B 131 ARG cc_start: 0.7043 (mpt-90) cc_final: 0.5473 (ttt180) REVERT: B 155 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5966 (mtp) REVERT: B 272 LYS cc_start: 0.6984 (tppp) cc_final: 0.6398 (ttpp) REVERT: B 279 GLU cc_start: 0.8143 (tt0) cc_final: 0.7775 (tt0) REVERT: B 331 MET cc_start: 0.6565 (ttp) cc_final: 0.6299 (ttp) REVERT: B 380 LYS cc_start: 0.7039 (mmtp) cc_final: 0.6568 (mmmt) REVERT: B 399 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7266 (tpt170) REVERT: C 71 MET cc_start: 0.6771 (mmm) cc_final: 0.6194 (mmm) REVERT: C 114 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6708 (mtmt) REVERT: C 126 ARG cc_start: 0.6451 (mtm110) cc_final: 0.5741 (mtm110) REVERT: C 131 ARG cc_start: 0.7042 (mpt-90) cc_final: 0.5472 (ttt180) REVERT: C 155 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5964 (mtp) REVERT: C 272 LYS cc_start: 0.6982 (tppp) cc_final: 0.6401 (ttpp) REVERT: C 279 GLU cc_start: 0.8142 (tt0) cc_final: 0.7775 (tt0) REVERT: C 331 MET cc_start: 0.6563 (ttp) cc_final: 0.6296 (ttp) REVERT: C 380 LYS cc_start: 0.7039 (mmtp) cc_final: 0.6567 (mmmt) REVERT: C 399 ARG cc_start: 0.8091 (mtm180) cc_final: 0.7267 (tpt170) REVERT: D 25 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7606 (m) REVERT: D 33 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7302 (mt-10) REVERT: D 71 MET cc_start: 0.6774 (mmm) cc_final: 0.6202 (mmm) REVERT: D 126 ARG cc_start: 0.6474 (mtm110) cc_final: 0.5748 (mtm110) REVERT: D 131 ARG cc_start: 0.7044 (mpt-90) cc_final: 0.5473 (ttt180) REVERT: D 155 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5965 (mtp) REVERT: D 272 LYS cc_start: 0.6983 (tppp) cc_final: 0.6398 (ttpp) REVERT: D 279 GLU cc_start: 0.8197 (tt0) cc_final: 0.7921 (tt0) REVERT: D 331 MET cc_start: 0.6540 (ttp) cc_final: 0.6268 (ttp) REVERT: D 380 LYS cc_start: 0.7037 (mmtp) cc_final: 0.6567 (mmmt) REVERT: D 399 ARG cc_start: 0.8093 (mtm180) cc_final: 0.7270 (tpt170) outliers start: 42 outliers final: 22 residues processed: 174 average time/residue: 1.3657 time to fit residues: 255.9719 Evaluate side-chains 172 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12236 Z= 0.160 Angle : 0.408 5.007 16596 Z= 0.225 Chirality : 0.034 0.131 1988 Planarity : 0.003 0.027 2032 Dihedral : 3.468 13.098 1656 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.61 % Allowed : 18.50 % Favored : 79.89 % 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: 3.32 (0.21), residues: 1504 helix: 2.71 (0.13), residues: 1264 sheet: 1.38 (0.66), residues: 48 loop : -1.39 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.001 0.000 HIS C 349 PHE 0.010 0.001 PHE A 11 TYR 0.006 0.001 TYR C 96 ARG 0.002 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.171 Fit side-chains REVERT: A 25 VAL cc_start: 0.7901 (p) cc_final: 0.7688 (m) REVERT: A 33 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 43 TYR cc_start: 0.8418 (t80) cc_final: 0.8193 (t80) REVERT: A 51 MET cc_start: 0.8223 (tpp) cc_final: 0.7958 (mmt) REVERT: A 126 ARG cc_start: 0.6334 (mtm110) cc_final: 0.5667 (mtm110) REVERT: A 131 ARG cc_start: 0.7014 (tpt-90) cc_final: 0.5436 (ttt180) REVERT: A 173 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.5394 (m-70) REVERT: A 272 LYS cc_start: 0.7020 (tppp) cc_final: 0.6458 (ttpp) REVERT: A 279 GLU cc_start: 0.8093 (tt0) cc_final: 0.7667 (tt0) REVERT: A 290 ASN cc_start: 0.8488 (t0) cc_final: 0.8131 (t0) REVERT: A 331 MET cc_start: 0.6465 (ttp) cc_final: 0.6204 (ttp) REVERT: A 364 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6729 (mm-30) REVERT: A 380 LYS cc_start: 0.6985 (mmtp) cc_final: 0.6525 (mmmt) REVERT: A 399 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7225 (tpt170) REVERT: A 410 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8507 (m) REVERT: B 25 VAL cc_start: 0.7901 (p) cc_final: 0.7687 (m) REVERT: B 33 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7233 (mt-10) REVERT: B 43 TYR cc_start: 0.8419 (t80) cc_final: 0.8194 (t80) REVERT: B 51 MET cc_start: 0.8220 (tpp) cc_final: 0.7954 (mmt) REVERT: B 126 ARG cc_start: 0.6335 (mtm110) cc_final: 0.5661 (mtm110) REVERT: B 131 ARG cc_start: 0.7017 (tpt-90) cc_final: 0.5463 (ttt180) REVERT: B 173 HIS cc_start: 0.6330 (OUTLIER) cc_final: 0.5406 (m-70) REVERT: B 272 LYS cc_start: 0.7019 (tppp) cc_final: 0.6454 (ttpp) REVERT: B 279 GLU cc_start: 0.8090 (tt0) cc_final: 0.7666 (tt0) REVERT: B 290 ASN cc_start: 0.8492 (t0) cc_final: 0.8135 (t0) REVERT: B 331 MET cc_start: 0.6447 (ttp) cc_final: 0.6171 (ttp) REVERT: B 364 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6734 (mm-30) REVERT: B 380 LYS cc_start: 0.6984 (mmtp) cc_final: 0.6524 (mmmt) REVERT: B 399 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7238 (tpt170) REVERT: C 43 TYR cc_start: 0.8420 (t80) cc_final: 0.8199 (t80) REVERT: C 51 MET cc_start: 0.8222 (tpp) cc_final: 0.7957 (mmt) REVERT: C 126 ARG cc_start: 0.6354 (mtm110) cc_final: 0.5665 (mtm110) REVERT: C 131 ARG cc_start: 0.7019 (tpt-90) cc_final: 0.5465 (ttt180) REVERT: C 173 HIS cc_start: 0.6326 (OUTLIER) cc_final: 0.5401 (m-70) REVERT: C 272 LYS cc_start: 0.7021 (tppp) cc_final: 0.6458 (ttpp) REVERT: C 279 GLU cc_start: 0.8092 (tt0) cc_final: 0.7666 (tt0) REVERT: C 290 ASN cc_start: 0.8492 (t0) cc_final: 0.8135 (t0) REVERT: C 331 MET cc_start: 0.6448 (ttp) cc_final: 0.6170 (ttp) REVERT: C 364 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6723 (mm-30) REVERT: C 380 LYS cc_start: 0.6984 (mmtp) cc_final: 0.6525 (mmmt) REVERT: C 399 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7238 (tpt170) REVERT: D 25 VAL cc_start: 0.7902 (p) cc_final: 0.7687 (m) REVERT: D 33 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7233 (mt-10) REVERT: D 43 TYR cc_start: 0.8419 (t80) cc_final: 0.8194 (t80) REVERT: D 51 MET cc_start: 0.8224 (tpp) cc_final: 0.7958 (mmt) REVERT: D 126 ARG cc_start: 0.6334 (mtm110) cc_final: 0.5667 (mtm110) REVERT: D 131 ARG cc_start: 0.7020 (tpt-90) cc_final: 0.5465 (ttt180) REVERT: D 173 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5403 (m-70) REVERT: D 272 LYS cc_start: 0.7019 (tppp) cc_final: 0.6456 (ttpp) REVERT: D 279 GLU cc_start: 0.8149 (tt0) cc_final: 0.7822 (tt0) REVERT: D 290 ASN cc_start: 0.8488 (t0) cc_final: 0.8130 (t0) REVERT: D 331 MET cc_start: 0.6463 (ttp) cc_final: 0.6198 (ttp) REVERT: D 364 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6724 (mm-30) REVERT: D 380 LYS cc_start: 0.6982 (mmtp) cc_final: 0.6523 (mmmt) REVERT: D 399 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7243 (tpt170) outliers start: 21 outliers final: 4 residues processed: 177 average time/residue: 1.2841 time to fit residues: 246.0455 Evaluate side-chains 173 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12236 Z= 0.163 Angle : 0.404 5.020 16596 Z= 0.222 Chirality : 0.035 0.132 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.391 12.279 1656 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.99 % Allowed : 19.11 % Favored : 78.90 % 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: 3.52 (0.21), residues: 1504 helix: 2.85 (0.13), residues: 1264 sheet: 1.28 (0.62), residues: 48 loop : -1.32 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.002 0.000 HIS D 337 PHE 0.009 0.001 PHE B 11 TYR 0.008 0.001 TYR A 175 ARG 0.002 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.431 Fit side-chains REVERT: A 25 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7636 (m) REVERT: A 33 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 51 MET cc_start: 0.8236 (tpp) cc_final: 0.7938 (mmt) REVERT: A 126 ARG cc_start: 0.6342 (mtm110) cc_final: 0.5586 (mtm110) REVERT: A 131 ARG cc_start: 0.7019 (tpt-90) cc_final: 0.5428 (ttt180) REVERT: A 173 HIS cc_start: 0.6216 (OUTLIER) cc_final: 0.5244 (m-70) REVERT: A 272 LYS cc_start: 0.7090 (tppp) cc_final: 0.6585 (ttpp) REVERT: A 279 GLU cc_start: 0.8076 (tt0) cc_final: 0.7647 (tt0) REVERT: A 290 ASN cc_start: 0.8520 (t0) cc_final: 0.8162 (t0) REVERT: A 331 MET cc_start: 0.6526 (ttp) cc_final: 0.6250 (ttp) REVERT: A 380 LYS cc_start: 0.7005 (mmtp) cc_final: 0.6537 (mmmt) REVERT: A 399 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7228 (tpt170) REVERT: B 25 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7548 (m) REVERT: B 33 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7227 (mt-10) REVERT: B 51 MET cc_start: 0.8233 (tpp) cc_final: 0.7934 (mmt) REVERT: B 126 ARG cc_start: 0.6349 (mtm110) cc_final: 0.5667 (mtm110) REVERT: B 131 ARG cc_start: 0.7022 (tpt-90) cc_final: 0.5456 (ttt180) REVERT: B 173 HIS cc_start: 0.6208 (OUTLIER) cc_final: 0.5267 (m-70) REVERT: B 272 LYS cc_start: 0.7089 (tppp) cc_final: 0.6581 (ttpp) REVERT: B 279 GLU cc_start: 0.8073 (tt0) cc_final: 0.7645 (tt0) REVERT: B 290 ASN cc_start: 0.8522 (t0) cc_final: 0.8171 (t0) REVERT: B 331 MET cc_start: 0.6497 (ttp) cc_final: 0.6220 (ttp) REVERT: B 380 LYS cc_start: 0.7001 (mmtp) cc_final: 0.6538 (mmmt) REVERT: B 399 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7239 (tpt170) REVERT: B 410 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8517 (m) REVERT: C 51 MET cc_start: 0.8236 (tpp) cc_final: 0.7937 (mmt) REVERT: C 126 ARG cc_start: 0.6349 (mtm110) cc_final: 0.5657 (mtm110) REVERT: C 131 ARG cc_start: 0.7022 (tpt-90) cc_final: 0.5457 (ttt180) REVERT: C 173 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5265 (m-70) REVERT: C 272 LYS cc_start: 0.7090 (tppp) cc_final: 0.6584 (ttpp) REVERT: C 279 GLU cc_start: 0.8073 (tt0) cc_final: 0.7643 (tt0) REVERT: C 290 ASN cc_start: 0.8523 (t0) cc_final: 0.8165 (t0) REVERT: C 331 MET cc_start: 0.6496 (ttp) cc_final: 0.6220 (ttp) REVERT: C 380 LYS cc_start: 0.6999 (mmtp) cc_final: 0.6535 (mmmt) REVERT: C 399 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7239 (tpt170) REVERT: C 410 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8517 (m) REVERT: D 25 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7636 (m) REVERT: D 33 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7232 (mt-10) REVERT: D 51 MET cc_start: 0.8251 (tpp) cc_final: 0.7956 (mmt) REVERT: D 126 ARG cc_start: 0.6346 (mtm110) cc_final: 0.5640 (mtm110) REVERT: D 131 ARG cc_start: 0.7026 (tpt-90) cc_final: 0.5458 (ttt180) REVERT: D 173 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5265 (m-70) REVERT: D 272 LYS cc_start: 0.7088 (tppp) cc_final: 0.6583 (ttpp) REVERT: D 279 GLU cc_start: 0.8123 (tt0) cc_final: 0.7800 (tt0) REVERT: D 290 ASN cc_start: 0.8520 (t0) cc_final: 0.8162 (t0) REVERT: D 331 MET cc_start: 0.6526 (ttp) cc_final: 0.6255 (ttp) REVERT: D 380 LYS cc_start: 0.7001 (mmtp) cc_final: 0.6536 (mmmt) REVERT: D 399 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7241 (tpt170) REVERT: D 410 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8519 (m) outliers start: 26 outliers final: 4 residues processed: 174 average time/residue: 1.2639 time to fit residues: 238.5153 Evaluate side-chains 174 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 383 GLN B 171 ASN B 383 GLN C 171 ASN C 383 GLN D 171 ASN D 383 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12236 Z= 0.257 Angle : 0.455 5.334 16596 Z= 0.249 Chirality : 0.037 0.131 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.566 12.787 1656 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.75 % Allowed : 17.89 % Favored : 79.36 % 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: 3.12 (0.20), residues: 1504 helix: 2.60 (0.13), residues: 1264 sheet: 0.62 (0.61), residues: 48 loop : -1.48 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 38 HIS 0.003 0.001 HIS C 337 PHE 0.011 0.002 PHE D 392 TYR 0.010 0.001 TYR B 175 ARG 0.003 0.000 ARG D 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.360 Fit side-chains REVERT: A 33 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 51 MET cc_start: 0.8299 (tpp) cc_final: 0.8004 (mmt) REVERT: A 71 MET cc_start: 0.6627 (mmm) cc_final: 0.6077 (mmm) REVERT: A 126 ARG cc_start: 0.6483 (mtm110) cc_final: 0.5729 (mtm110) REVERT: A 131 ARG cc_start: 0.7061 (tpt-90) cc_final: 0.5454 (tmt-80) REVERT: A 272 LYS cc_start: 0.7060 (tppp) cc_final: 0.6521 (ttpp) REVERT: A 279 GLU cc_start: 0.8192 (tt0) cc_final: 0.7892 (tt0) REVERT: A 331 MET cc_start: 0.6550 (ttp) cc_final: 0.6273 (ttp) REVERT: A 380 LYS cc_start: 0.7033 (mmtp) cc_final: 0.6548 (mmmt) REVERT: A 399 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7249 (tpt170) REVERT: A 410 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8502 (m) REVERT: B 33 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7237 (mt-10) REVERT: B 51 MET cc_start: 0.8300 (tpp) cc_final: 0.8006 (mmt) REVERT: B 71 MET cc_start: 0.6622 (mmm) cc_final: 0.6073 (mmm) REVERT: B 126 ARG cc_start: 0.6440 (mtm110) cc_final: 0.5744 (mtm110) REVERT: B 131 ARG cc_start: 0.7058 (tpt-90) cc_final: 0.5487 (ttt180) REVERT: B 272 LYS cc_start: 0.7058 (tppp) cc_final: 0.6517 (ttpp) REVERT: B 279 GLU cc_start: 0.8202 (tt0) cc_final: 0.7900 (tt0) REVERT: B 331 MET cc_start: 0.6542 (ttp) cc_final: 0.6272 (ttp) REVERT: B 380 LYS cc_start: 0.7030 (mmtp) cc_final: 0.6548 (mmmt) REVERT: B 399 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7259 (tpt170) REVERT: B 410 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8501 (m) REVERT: C 51 MET cc_start: 0.8299 (tpp) cc_final: 0.8005 (mmt) REVERT: C 71 MET cc_start: 0.6621 (mmm) cc_final: 0.6065 (mmm) REVERT: C 126 ARG cc_start: 0.6440 (mtm110) cc_final: 0.5753 (mtm110) REVERT: C 131 ARG cc_start: 0.7059 (tpt-90) cc_final: 0.5449 (tmt-80) REVERT: C 272 LYS cc_start: 0.7059 (tppp) cc_final: 0.6518 (ttpp) REVERT: C 279 GLU cc_start: 0.8183 (tt0) cc_final: 0.7903 (tt0) REVERT: C 331 MET cc_start: 0.6536 (ttp) cc_final: 0.6266 (ttp) REVERT: C 380 LYS cc_start: 0.7029 (mmtp) cc_final: 0.6548 (mmmt) REVERT: C 399 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7257 (tpt170) REVERT: C 410 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8501 (m) REVERT: D 33 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7180 (mt-10) REVERT: D 51 MET cc_start: 0.8311 (tpp) cc_final: 0.8013 (mmt) REVERT: D 71 MET cc_start: 0.6626 (mmm) cc_final: 0.6074 (mmm) REVERT: D 126 ARG cc_start: 0.6485 (mtm110) cc_final: 0.5730 (mtm110) REVERT: D 131 ARG cc_start: 0.7064 (tpt-90) cc_final: 0.5492 (ttt180) REVERT: D 272 LYS cc_start: 0.7058 (tppp) cc_final: 0.6519 (ttpp) REVERT: D 279 GLU cc_start: 0.8207 (tt0) cc_final: 0.7942 (tt0) REVERT: D 331 MET cc_start: 0.6551 (ttp) cc_final: 0.6274 (ttp) REVERT: D 380 LYS cc_start: 0.7031 (mmtp) cc_final: 0.6547 (mmmt) REVERT: D 399 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7295 (tpt170) REVERT: D 410 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8501 (m) outliers start: 36 outliers final: 9 residues processed: 178 average time/residue: 1.2983 time to fit residues: 250.1350 Evaluate side-chains 166 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 383 GLN B 189 GLN B 383 GLN C 189 GLN C 383 GLN D 189 GLN D 383 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12236 Z= 0.213 Angle : 0.432 5.172 16596 Z= 0.237 Chirality : 0.036 0.131 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.542 13.725 1656 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.14 % Allowed : 18.96 % Favored : 78.90 % 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: 3.19 (0.20), residues: 1504 helix: 2.66 (0.13), residues: 1264 sheet: 0.55 (0.61), residues: 48 loop : -1.48 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.002 0.000 HIS C 337 PHE 0.010 0.002 PHE C 11 TYR 0.008 0.001 TYR C 175 ARG 0.001 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.297 Fit side-chains REVERT: A 33 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7249 (mt-10) REVERT: A 51 MET cc_start: 0.8339 (tpp) cc_final: 0.8061 (mmt) REVERT: A 71 MET cc_start: 0.6663 (mmm) cc_final: 0.6133 (mmm) REVERT: A 126 ARG cc_start: 0.6401 (mtm110) cc_final: 0.5627 (mtm110) REVERT: A 131 ARG cc_start: 0.7063 (tpt-90) cc_final: 0.5447 (tmt-80) REVERT: A 173 HIS cc_start: 0.6227 (OUTLIER) cc_final: 0.5230 (m-70) REVERT: A 272 LYS cc_start: 0.7048 (tppp) cc_final: 0.6517 (ttpp) REVERT: A 279 GLU cc_start: 0.8200 (tt0) cc_final: 0.7889 (tt0) REVERT: A 283 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8278 (mttt) REVERT: A 331 MET cc_start: 0.6532 (ttp) cc_final: 0.6257 (ttp) REVERT: A 380 LYS cc_start: 0.7020 (mmtp) cc_final: 0.6524 (mmmt) REVERT: A 399 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7267 (tpt170) REVERT: A 410 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8507 (m) REVERT: B 33 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7246 (mt-10) REVERT: B 51 MET cc_start: 0.8313 (tpp) cc_final: 0.8032 (mmt) REVERT: B 71 MET cc_start: 0.6662 (mmm) cc_final: 0.6131 (mmm) REVERT: B 126 ARG cc_start: 0.6358 (mtm110) cc_final: 0.5657 (mtm110) REVERT: B 131 ARG cc_start: 0.7062 (tpt-90) cc_final: 0.5444 (tmt-80) REVERT: B 173 HIS cc_start: 0.6220 (OUTLIER) cc_final: 0.5254 (m-70) REVERT: B 272 LYS cc_start: 0.7047 (tppp) cc_final: 0.6514 (ttpp) REVERT: B 279 GLU cc_start: 0.8200 (tt0) cc_final: 0.7882 (tt0) REVERT: B 331 MET cc_start: 0.6489 (ttp) cc_final: 0.6218 (ttp) REVERT: B 380 LYS cc_start: 0.7020 (mmtp) cc_final: 0.6526 (mmmt) REVERT: B 399 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7278 (tpt170) REVERT: B 410 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8504 (m) REVERT: C 51 MET cc_start: 0.8347 (tpp) cc_final: 0.8068 (mmt) REVERT: C 71 MET cc_start: 0.6625 (mmm) cc_final: 0.6089 (mmm) REVERT: C 126 ARG cc_start: 0.6359 (mtm110) cc_final: 0.5658 (mtm110) REVERT: C 131 ARG cc_start: 0.7062 (tpt-90) cc_final: 0.5445 (tmt-80) REVERT: C 173 HIS cc_start: 0.6216 (OUTLIER) cc_final: 0.5248 (m-70) REVERT: C 272 LYS cc_start: 0.7047 (tppp) cc_final: 0.6516 (ttpp) REVERT: C 279 GLU cc_start: 0.8191 (tt0) cc_final: 0.7873 (tt0) REVERT: C 290 ASN cc_start: 0.8545 (t0) cc_final: 0.8167 (t0) REVERT: C 331 MET cc_start: 0.6490 (ttp) cc_final: 0.6219 (ttp) REVERT: C 380 LYS cc_start: 0.7020 (mmtp) cc_final: 0.6526 (mmmt) REVERT: C 399 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7276 (tpt170) REVERT: C 410 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8505 (m) REVERT: D 33 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7249 (mt-10) REVERT: D 51 MET cc_start: 0.8348 (tpp) cc_final: 0.8070 (mmt) REVERT: D 71 MET cc_start: 0.6635 (mmm) cc_final: 0.6105 (mmm) REVERT: D 126 ARG cc_start: 0.6401 (mtm110) cc_final: 0.5626 (mtm110) REVERT: D 131 ARG cc_start: 0.7065 (tpt-90) cc_final: 0.5447 (tmt-80) REVERT: D 173 HIS cc_start: 0.6218 (OUTLIER) cc_final: 0.5251 (m-70) REVERT: D 272 LYS cc_start: 0.7046 (tppp) cc_final: 0.6516 (ttpp) REVERT: D 279 GLU cc_start: 0.8214 (tt0) cc_final: 0.7923 (tt0) REVERT: D 331 MET cc_start: 0.6531 (ttp) cc_final: 0.6256 (ttp) REVERT: D 380 LYS cc_start: 0.7020 (mmtp) cc_final: 0.6524 (mmmt) REVERT: D 399 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7281 (tpt170) REVERT: D 410 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8504 (m) outliers start: 28 outliers final: 11 residues processed: 171 average time/residue: 1.2203 time to fit residues: 226.8356 Evaluate side-chains 173 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12236 Z= 0.175 Angle : 0.414 5.099 16596 Z= 0.228 Chirality : 0.035 0.131 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.480 14.059 1656 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.75 % Allowed : 18.50 % Favored : 78.75 % 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: 3.34 (0.20), residues: 1504 helix: 2.77 (0.13), residues: 1264 sheet: 0.32 (0.52), residues: 48 loop : -1.44 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 154 HIS 0.001 0.000 HIS A 349 PHE 0.010 0.001 PHE D 422 TYR 0.007 0.001 TYR C 175 ARG 0.001 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 1.315 Fit side-chains REVERT: A 33 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7219 (mt-10) REVERT: A 51 MET cc_start: 0.8314 (tpp) cc_final: 0.8050 (mmt) REVERT: A 71 MET cc_start: 0.6629 (mmm) cc_final: 0.6103 (mmm) REVERT: A 126 ARG cc_start: 0.6400 (mtm110) cc_final: 0.5630 (mtm110) REVERT: A 131 ARG cc_start: 0.7053 (tpt-90) cc_final: 0.5413 (tmt-80) REVERT: A 173 HIS cc_start: 0.6208 (OUTLIER) cc_final: 0.5215 (m-70) REVERT: A 272 LYS cc_start: 0.7040 (tppp) cc_final: 0.6526 (ttpp) REVERT: A 279 GLU cc_start: 0.8089 (tt0) cc_final: 0.7662 (tt0) REVERT: A 283 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8240 (mttt) REVERT: A 290 ASN cc_start: 0.8558 (t0) cc_final: 0.8204 (t0) REVERT: A 331 MET cc_start: 0.6524 (ttp) cc_final: 0.6247 (ttp) REVERT: A 380 LYS cc_start: 0.7012 (mmtp) cc_final: 0.6523 (mmmt) REVERT: A 399 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7244 (tpt170) REVERT: A 410 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8500 (m) REVERT: B 33 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7220 (mt-10) REVERT: B 51 MET cc_start: 0.8284 (tpp) cc_final: 0.8018 (mmt) REVERT: B 71 MET cc_start: 0.6615 (mmm) cc_final: 0.6088 (mmm) REVERT: B 126 ARG cc_start: 0.6408 (mtm110) cc_final: 0.5670 (mtm110) REVERT: B 131 ARG cc_start: 0.7055 (tpt-90) cc_final: 0.5410 (tmt-80) REVERT: B 173 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5232 (m-70) REVERT: B 272 LYS cc_start: 0.7037 (tppp) cc_final: 0.6522 (ttpp) REVERT: B 279 GLU cc_start: 0.8086 (tt0) cc_final: 0.7660 (tt0) REVERT: B 283 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8242 (mttt) REVERT: B 290 ASN cc_start: 0.8558 (t0) cc_final: 0.8204 (t0) REVERT: B 331 MET cc_start: 0.6493 (ttp) cc_final: 0.6223 (ttp) REVERT: B 380 LYS cc_start: 0.7010 (mmtp) cc_final: 0.6522 (mmmt) REVERT: B 399 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7256 (tpt170) REVERT: B 410 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8497 (m) REVERT: C 51 MET cc_start: 0.8313 (tpp) cc_final: 0.8046 (mmt) REVERT: C 126 ARG cc_start: 0.6412 (mtm110) cc_final: 0.5671 (mtm110) REVERT: C 131 ARG cc_start: 0.7055 (tpt-90) cc_final: 0.5411 (tmt-80) REVERT: C 173 HIS cc_start: 0.6236 (OUTLIER) cc_final: 0.5231 (m-70) REVERT: C 272 LYS cc_start: 0.7039 (tppp) cc_final: 0.6525 (ttpp) REVERT: C 279 GLU cc_start: 0.8088 (tt0) cc_final: 0.7661 (tt0) REVERT: C 283 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8274 (mttt) REVERT: C 290 ASN cc_start: 0.8561 (t0) cc_final: 0.8207 (t0) REVERT: C 331 MET cc_start: 0.6493 (ttp) cc_final: 0.6222 (ttp) REVERT: C 380 LYS cc_start: 0.7008 (mmtp) cc_final: 0.6521 (mmmt) REVERT: C 399 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7255 (tpt170) REVERT: C 410 SER cc_start: 0.8985 (OUTLIER) cc_final: 0.8499 (m) REVERT: D 33 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 51 MET cc_start: 0.8314 (tpp) cc_final: 0.8051 (mmt) REVERT: D 71 MET cc_start: 0.6625 (mmm) cc_final: 0.6098 (mmm) REVERT: D 126 ARG cc_start: 0.6401 (mtm110) cc_final: 0.5630 (mtm110) REVERT: D 131 ARG cc_start: 0.7058 (tpt-90) cc_final: 0.5417 (tmt-80) REVERT: D 173 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.5229 (m-70) REVERT: D 272 LYS cc_start: 0.7037 (tppp) cc_final: 0.6525 (ttpp) REVERT: D 279 GLU cc_start: 0.8182 (tt0) cc_final: 0.7815 (tt0) REVERT: D 290 ASN cc_start: 0.8558 (t0) cc_final: 0.8202 (t0) REVERT: D 331 MET cc_start: 0.6522 (ttp) cc_final: 0.6249 (ttp) REVERT: D 380 LYS cc_start: 0.7008 (mmtp) cc_final: 0.6520 (mmmt) REVERT: D 399 ARG cc_start: 0.7962 (mtm180) cc_final: 0.7275 (tpt170) REVERT: D 410 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8498 (m) outliers start: 36 outliers final: 8 residues processed: 187 average time/residue: 1.2229 time to fit residues: 248.7129 Evaluate side-chains 183 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12236 Z= 0.162 Angle : 0.405 5.025 16596 Z= 0.224 Chirality : 0.035 0.131 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.434 13.196 1656 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.45 % Allowed : 20.41 % Favored : 78.13 % 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: 3.44 (0.20), residues: 1504 helix: 2.84 (0.13), residues: 1264 sheet: 0.21 (0.50), residues: 48 loop : -1.39 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 154 HIS 0.001 0.000 HIS B 349 PHE 0.009 0.001 PHE C 11 TYR 0.006 0.001 TYR A 175 ARG 0.001 0.000 ARG A 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.407 Fit side-chains REVERT: A 33 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 51 MET cc_start: 0.8261 (tpp) cc_final: 0.7997 (mmt) REVERT: A 126 ARG cc_start: 0.6411 (mtm110) cc_final: 0.5611 (mtm110) REVERT: A 131 ARG cc_start: 0.7052 (tpt-90) cc_final: 0.5419 (tmt-80) REVERT: A 173 HIS cc_start: 0.6273 (OUTLIER) cc_final: 0.5229 (m-70) REVERT: A 272 LYS cc_start: 0.7029 (tppp) cc_final: 0.6538 (ttpp) REVERT: A 279 GLU cc_start: 0.8148 (tt0) cc_final: 0.7848 (tt0) REVERT: A 283 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8218 (mttt) REVERT: A 290 ASN cc_start: 0.8537 (t0) cc_final: 0.8209 (t0) REVERT: A 331 MET cc_start: 0.6516 (ttp) cc_final: 0.6242 (ttp) REVERT: A 380 LYS cc_start: 0.6968 (mmtp) cc_final: 0.6506 (mmmt) REVERT: A 399 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7242 (tpt170) REVERT: A 410 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8525 (m) REVERT: B 33 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7228 (mt-10) REVERT: B 51 MET cc_start: 0.8260 (tpp) cc_final: 0.7996 (mmt) REVERT: B 126 ARG cc_start: 0.6406 (mtm110) cc_final: 0.5611 (mtm110) REVERT: B 131 ARG cc_start: 0.7052 (tpt-90) cc_final: 0.5414 (tmt-80) REVERT: B 173 HIS cc_start: 0.6181 (OUTLIER) cc_final: 0.5142 (m-70) REVERT: B 272 LYS cc_start: 0.7028 (tppp) cc_final: 0.6531 (ttpp) REVERT: B 279 GLU cc_start: 0.8144 (tt0) cc_final: 0.7846 (tt0) REVERT: B 283 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8235 (mttt) REVERT: B 290 ASN cc_start: 0.8535 (t0) cc_final: 0.8206 (t0) REVERT: B 331 MET cc_start: 0.6490 (ttp) cc_final: 0.6220 (ttp) REVERT: B 380 LYS cc_start: 0.6968 (mmtp) cc_final: 0.6504 (mmmt) REVERT: B 399 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7254 (tpt170) REVERT: B 410 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8523 (m) REVERT: C 51 MET cc_start: 0.8307 (tpp) cc_final: 0.8043 (mmt) REVERT: C 126 ARG cc_start: 0.6408 (mtm110) cc_final: 0.5613 (mtm110) REVERT: C 131 ARG cc_start: 0.7051 (tpt-90) cc_final: 0.5412 (tmt-80) REVERT: C 173 HIS cc_start: 0.6179 (OUTLIER) cc_final: 0.5138 (m-70) REVERT: C 272 LYS cc_start: 0.7027 (tppp) cc_final: 0.6535 (ttpp) REVERT: C 279 GLU cc_start: 0.8147 (tt0) cc_final: 0.7848 (tt0) REVERT: C 283 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8232 (mttt) REVERT: C 290 ASN cc_start: 0.8541 (t0) cc_final: 0.8210 (t0) REVERT: C 331 MET cc_start: 0.6490 (ttp) cc_final: 0.6218 (ttp) REVERT: C 380 LYS cc_start: 0.6969 (mmtp) cc_final: 0.6506 (mmmt) REVERT: C 399 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7254 (tpt170) REVERT: C 410 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8524 (m) REVERT: D 33 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7227 (mt-10) REVERT: D 51 MET cc_start: 0.8306 (tpp) cc_final: 0.8045 (mmt) REVERT: D 126 ARG cc_start: 0.6409 (mtm110) cc_final: 0.5610 (mtm110) REVERT: D 131 ARG cc_start: 0.7053 (tpt-90) cc_final: 0.5455 (ttt180) REVERT: D 173 HIS cc_start: 0.6180 (OUTLIER) cc_final: 0.5139 (m-70) REVERT: D 272 LYS cc_start: 0.7025 (tppp) cc_final: 0.6535 (ttpp) REVERT: D 279 GLU cc_start: 0.8183 (tt0) cc_final: 0.7874 (tt0) REVERT: D 290 ASN cc_start: 0.8536 (t0) cc_final: 0.8206 (t0) REVERT: D 331 MET cc_start: 0.6521 (ttp) cc_final: 0.6251 (ttp) REVERT: D 380 LYS cc_start: 0.6967 (mmtp) cc_final: 0.6503 (mmmt) REVERT: D 399 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7256 (tpt170) REVERT: D 410 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8524 (m) outliers start: 19 outliers final: 8 residues processed: 179 average time/residue: 1.3071 time to fit residues: 253.5042 Evaluate side-chains 183 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 GLN C 383 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.161090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.118144 restraints weight = 11932.312| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.55 r_work: 0.3109 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12236 Z= 0.136 Angle : 0.389 4.801 16596 Z= 0.215 Chirality : 0.034 0.132 1988 Planarity : 0.002 0.026 2032 Dihedral : 3.362 13.255 1656 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.76 % Allowed : 20.03 % Favored : 78.21 % 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: 3.67 (0.21), residues: 1504 helix: 3.00 (0.13), residues: 1264 sheet: 0.19 (0.48), residues: 48 loop : -1.26 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 154 HIS 0.001 0.000 HIS A 278 PHE 0.009 0.001 PHE C 11 TYR 0.006 0.001 TYR C 96 ARG 0.001 0.000 ARG C 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4319.68 seconds wall clock time: 86 minutes 16.32 seconds (5176.32 seconds total)