Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/11_2022/6gx5_0077.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/11_2022/6gx5_0077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/11_2022/6gx5_0077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/11_2022/6gx5_0077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/11_2022/6gx5_0077.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/11_2022/6gx5_0077.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2133 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "B" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "C" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Time building chain proxies: 1.60, per 1000 atoms: 0.75 Number of scatterers: 2133 At special positions: 0 Unit cell: (110.4, 81.65, 40.25, 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 3 16.00 O 399 8.00 N 396 7.00 C 1335 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 306.2 milliseconds 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 87.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 255 through 260 removed outlier: 6.408A pdb=" N ASN A 255 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER C 258 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 257 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ILE C 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS A 259 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.637A pdb=" N THR A 263 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 266 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN A 265 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N HIS B 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS A 267 " --> pdb=" O HIS B 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 274 through 310 removed outlier: 6.458A pdb=" N VAL A 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL B 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 removed outlier: 7.035A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.462A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.266A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.123A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 336 through 354 removed outlier: 9.047A pdb=" N GLN A 336 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N VAL B 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N SER B 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LYS B 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU A 342 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASP B 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS B 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 346 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ARG B 349 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP A 348 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN B 351 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS B 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER A 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 337 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU C 338 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 339 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS C 340 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER A 341 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU C 342 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.787A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 369 through 377 removed outlier: 6.908A pdb=" N LYS A 370 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 363 1.32 - 1.44: 504 1.44 - 1.56: 1247 1.56 - 1.69: 49 1.69 - 1.81: 3 Bond restraints: 2166 Sorted by residual: bond pdb=" N GLN B 269 " pdb=" CA GLN B 269 " ideal model delta sigma weight residual 1.457 1.533 -0.076 1.41e-02 5.03e+03 2.92e+01 bond pdb=" N GLN A 269 " pdb=" CA GLN A 269 " ideal model delta sigma weight residual 1.457 1.532 -0.076 1.41e-02 5.03e+03 2.87e+01 bond pdb=" N GLN C 269 " pdb=" CA GLN C 269 " ideal model delta sigma weight residual 1.457 1.532 -0.075 1.41e-02 5.03e+03 2.84e+01 bond pdb=" N LEU B 376 " pdb=" CA LEU B 376 " ideal model delta sigma weight residual 1.454 1.519 -0.064 1.27e-02 6.20e+03 2.56e+01 bond pdb=" N LEU A 376 " pdb=" CA LEU A 376 " ideal model delta sigma weight residual 1.454 1.518 -0.064 1.27e-02 6.20e+03 2.52e+01 ... (remaining 2161 not shown) Histogram of bond angle deviations from ideal: 103.03 - 108.71: 147 108.71 - 114.39: 1209 114.39 - 120.07: 546 120.07 - 125.75: 969 125.75 - 131.43: 21 Bond angle restraints: 2892 Sorted by residual: angle pdb=" N LYS B 340 " pdb=" CA LYS B 340 " pdb=" C LYS B 340 " ideal model delta sigma weight residual 109.24 114.94 -5.70 1.67e+00 3.59e-01 1.17e+01 angle pdb=" N LYS A 340 " pdb=" CA LYS A 340 " pdb=" C LYS A 340 " ideal model delta sigma weight residual 109.24 114.92 -5.68 1.67e+00 3.59e-01 1.15e+01 angle pdb=" N LYS C 340 " pdb=" CA LYS C 340 " pdb=" C LYS C 340 " ideal model delta sigma weight residual 109.24 114.90 -5.66 1.67e+00 3.59e-01 1.15e+01 angle pdb=" N GLU C 338 " pdb=" CA GLU C 338 " pdb=" C GLU C 338 " ideal model delta sigma weight residual 108.76 114.44 -5.68 1.69e+00 3.50e-01 1.13e+01 angle pdb=" N GLU A 338 " pdb=" CA GLU A 338 " pdb=" C GLU A 338 " ideal model delta sigma weight residual 108.76 114.42 -5.66 1.69e+00 3.50e-01 1.12e+01 ... (remaining 2887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.95: 1103 13.95 - 27.90: 139 27.90 - 41.85: 63 41.85 - 55.80: 15 55.80 - 69.76: 6 Dihedral angle restraints: 1326 sinusoidal: 558 harmonic: 768 Sorted by residual: dihedral pdb=" CA ASP C 358 " pdb=" C ASP C 358 " pdb=" N ASN C 359 " pdb=" CA ASN C 359 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP B 358 " pdb=" C ASP B 358 " pdb=" N ASN B 359 " pdb=" CA ASN B 359 " ideal model delta harmonic sigma weight residual 180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP A 358 " pdb=" C ASP A 358 " pdb=" N ASN A 359 " pdb=" CA ASN A 359 " ideal model delta harmonic sigma weight residual -180.00 -161.89 -18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 1323 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.066: 162 0.066 - 0.132: 90 0.132 - 0.198: 48 0.198 - 0.264: 6 0.264 - 0.330: 15 Chirality restraints: 321 Sorted by residual: chirality pdb=" CA PRO C 270 " pdb=" N PRO C 270 " pdb=" C PRO C 270 " pdb=" CB PRO C 270 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA PRO B 270 " pdb=" N PRO B 270 " pdb=" C PRO B 270 " pdb=" CB PRO B 270 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA PRO A 270 " pdb=" N PRO A 270 " pdb=" C PRO A 270 " pdb=" CB PRO A 270 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 318 not shown) Planarity restraints: 369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 363 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO B 364 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 330 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C HIS B 330 " -0.042 2.00e-02 2.50e+03 pdb=" O HIS B 330 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS B 331 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " -0.039 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 364 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.034 5.00e-02 4.00e+02 ... (remaining 366 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 1078 3.06 - 3.52: 1856 3.52 - 3.98: 3364 3.98 - 4.44: 3156 4.44 - 4.90: 6687 Nonbonded interactions: 16141 Sorted by model distance: nonbonded pdb=" O HIS A 268 " pdb=" N GLN C 269 " model vdw 2.596 2.520 nonbonded pdb=" N GLN A 269 " pdb=" O HIS B 268 " model vdw 2.597 2.520 nonbonded pdb=" OG1 THR B 361 " pdb=" OG1 THR B 373 " model vdw 2.629 2.440 nonbonded pdb=" OG1 THR C 361 " pdb=" OG1 THR C 373 " model vdw 2.629 2.440 nonbonded pdb=" OG1 THR A 361 " pdb=" OG1 THR A 373 " model vdw 2.630 2.440 ... (remaining 16136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 1335 2.51 5 N 396 2.21 5 O 399 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.880 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.010 Process input model: 11.700 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 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 : 0.017 0.076 2166 Z= 1.178 Angle : 1.199 8.660 2892 Z= 0.690 Chirality : 0.111 0.330 321 Planarity : 0.012 0.061 369 Dihedral : 16.090 69.756 840 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.50 (0.34), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.26), residues: 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.282 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 81 average time/residue: 0.3118 time to fit residues: 27.1317 Evaluate side-chains 67 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.282 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0265 time to fit residues: 0.4959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 2166 Z= 0.379 Angle : 0.635 6.122 2892 Z= 0.315 Chirality : 0.051 0.135 321 Planarity : 0.006 0.045 369 Dihedral : 5.102 21.022 285 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 2.88 % 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: -3.16 (0.36), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.28), residues: 276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.277 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 74 average time/residue: 0.2929 time to fit residues: 23.3526 Evaluate side-chains 60 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0253 time to fit residues: 0.4284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.0030 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 19 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 overall best weight: 0.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 2166 Z= 0.181 Angle : 0.562 5.253 2892 Z= 0.275 Chirality : 0.049 0.121 321 Planarity : 0.004 0.034 369 Dihedral : 4.606 18.093 285 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 2.06 % 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: -3.09 (0.37), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.29), residues: 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.3244 time to fit residues: 23.6264 Evaluate side-chains 62 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.253 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0368 time to fit residues: 0.4873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 2166 Z= 0.343 Angle : 0.620 6.978 2892 Z= 0.304 Chirality : 0.050 0.131 321 Planarity : 0.004 0.035 369 Dihedral : 4.792 18.432 285 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 1.65 % 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: -2.96 (0.39), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.30), residues: 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.279 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 69 average time/residue: 0.3188 time to fit residues: 23.6016 Evaluate side-chains 67 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0356 time to fit residues: 0.4887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.036 2166 Z= 0.374 Angle : 0.621 6.823 2892 Z= 0.305 Chirality : 0.051 0.129 321 Planarity : 0.004 0.033 369 Dihedral : 4.872 18.074 285 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 3.70 % 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: -2.87 (0.40), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.30), residues: 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.304 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 70 average time/residue: 0.3297 time to fit residues: 24.8582 Evaluate side-chains 69 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1018 time to fit residues: 0.8668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 2166 Z= 0.360 Angle : 0.621 5.943 2892 Z= 0.305 Chirality : 0.051 0.126 321 Planarity : 0.004 0.033 369 Dihedral : 4.878 17.326 285 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.82 % 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: -2.84 (0.40), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.290 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.3244 time to fit residues: 23.9960 Evaluate side-chains 67 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0478 time to fit residues: 0.4476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 2166 Z= 0.307 Angle : 0.618 5.776 2892 Z= 0.302 Chirality : 0.051 0.123 321 Planarity : 0.004 0.033 369 Dihedral : 4.836 16.729 285 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 2.06 % 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: -2.82 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.31), residues: 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.298 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.3131 time to fit residues: 24.5884 Evaluate side-chains 72 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0328 time to fit residues: 0.5449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 2166 Z= 0.372 Angle : 0.666 6.107 2892 Z= 0.323 Chirality : 0.051 0.128 321 Planarity : 0.004 0.030 369 Dihedral : 5.046 17.091 285 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.41 % 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: -2.83 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.3339 time to fit residues: 24.6835 Evaluate side-chains 68 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.0170 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 2166 Z= 0.238 Angle : 0.634 7.185 2892 Z= 0.305 Chirality : 0.050 0.121 321 Planarity : 0.004 0.032 369 Dihedral : 4.848 17.105 285 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 2.06 % 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: -2.84 (0.40), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.3061 time to fit residues: 23.3842 Evaluate side-chains 70 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0393 time to fit residues: 0.5176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 8 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 2166 Z= 0.296 Angle : 0.700 8.584 2892 Z= 0.330 Chirality : 0.051 0.123 321 Planarity : 0.004 0.032 369 Dihedral : 4.979 16.812 285 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 1.23 % 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: -2.83 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.338 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 70 average time/residue: 0.3499 time to fit residues: 26.3645 Evaluate side-chains 65 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.0670 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060025 restraints weight = 3601.257| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.48 r_work: 0.2957 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work: 0.2936 rms_B_bonded: 2.24 restraints_weight: 0.1250 r_work: 0.2925 rms_B_bonded: 2.28 restraints_weight: 0.0625 r_work: 0.2913 rms_B_bonded: 2.34 restraints_weight: 0.0312 r_work: 0.2901 rms_B_bonded: 2.42 restraints_weight: 0.0156 r_work: 0.2889 rms_B_bonded: 2.52 restraints_weight: 0.0078 r_work: 0.2876 rms_B_bonded: 2.65 restraints_weight: 0.0039 r_work: 0.2862 rms_B_bonded: 2.79 restraints_weight: 0.0020 r_work: 0.2848 rms_B_bonded: 2.94 restraints_weight: 0.0010 r_work: 0.2832 rms_B_bonded: 3.12 restraints_weight: 0.0005 r_work: 0.2816 rms_B_bonded: 3.33 restraints_weight: 0.0002 r_work: 0.2799 rms_B_bonded: 3.55 restraints_weight: 0.0001 r_work: 0.2781 rms_B_bonded: 3.80 restraints_weight: 0.0001 r_work: 0.2762 rms_B_bonded: 4.07 restraints_weight: 0.0000 r_work: 0.2741 rms_B_bonded: 4.38 restraints_weight: 0.0000 r_work: 0.2719 rms_B_bonded: 4.71 restraints_weight: 0.0000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 2166 Z= 0.361 Angle : 0.712 8.596 2892 Z= 0.340 Chirality : 0.052 0.124 321 Planarity : 0.004 0.030 369 Dihedral : 5.182 17.319 285 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 1.23 % 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: -2.84 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.31), residues: 276 =============================================================================== Job complete usr+sys time: 1237.32 seconds wall clock time: 22 minutes 43.47 seconds (1363.47 seconds total)