Starting phenix.real_space_refine on Thu Dec 7 16:09:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/12_2023/6gx5_0077.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/12_2023/6gx5_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_0077/12_2023/6gx5_0077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/12_2023/6gx5_0077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/12_2023/6gx5_0077.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gx5_0077/12_2023/6gx5_0077.pdb" } resolution = 3.2 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= 0.002 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 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. 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-1.21rc1-5172/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: 1.64, per 1000 atoms: 0.77 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: 0.77 Conformation dependent library (CDL) restraints added in 388.8 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: 0.29 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: 0.48 Time building geometry restraints manager: 0.84 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 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: 0.780 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: 3.860 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 % Allowed : 9.88 % Favored : 85.19 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.005 HIS C 362 PHE 0.038 0.011 PHE C 346 TYR 0.025 0.009 TYR C 310 ARG 0.002 0.001 ARG B 349 *********************** 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 : 0.259 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 81 average time/residue: 0.3131 time to fit residues: 27.3136 Evaluate side-chains 67 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.234 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0245 time to fit residues: 0.4238 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 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** B 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2166 Z= 0.370 Angle : 0.628 6.127 2892 Z= 0.311 Chirality : 0.050 0.133 321 Planarity : 0.006 0.044 369 Dihedral : 5.088 21.006 285 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.88 % Allowed : 18.11 % Favored : 79.01 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.015 0.003 PHE A 378 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** 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 : 0.232 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 74 average time/residue: 0.3000 time to fit residues: 23.8354 Evaluate side-chains 60 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0279 time to fit residues: 0.4093 ------------------------------------------------------------------------------- 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: 0.3980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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: 0.8518 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2166 Z= 0.234 Angle : 0.570 5.478 2892 Z= 0.281 Chirality : 0.050 0.123 321 Planarity : 0.004 0.036 369 Dihedral : 4.686 18.080 285 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.23 % Allowed : 23.05 % Favored : 75.72 % 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: -3.06 (0.38), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.29), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.007 0.001 PHE A 378 TYR 0.007 0.001 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** 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: 3 poor density : 69 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 0.3325 time to fit residues: 24.9012 Evaluate side-chains 61 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.233 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0331 time to fit residues: 0.4088 ------------------------------------------------------------------------------- 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: 0.0770 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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: 0.8513 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2166 Z= 0.236 Angle : 0.580 6.371 2892 Z= 0.281 Chirality : 0.049 0.122 321 Planarity : 0.004 0.033 369 Dihedral : 4.592 17.002 285 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.23 % Allowed : 23.05 % Favored : 75.72 % 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 (0.29), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.006 0.001 PHE A 378 TYR 0.006 0.001 TYR C 310 ARG 0.000 0.000 ARG B 349 *********************** 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: 3 poor density : 69 time to evaluate : 0.253 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 0.3295 time to fit residues: 24.6676 Evaluate side-chains 68 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0366 time to fit residues: 0.4515 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.8554 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 2166 Z= 0.533 Angle : 0.688 7.064 2892 Z= 0.342 Chirality : 0.053 0.145 321 Planarity : 0.005 0.034 369 Dihedral : 5.102 18.859 285 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.47 % Allowed : 20.99 % Favored : 76.54 % 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 : -2.16 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 362 PHE 0.013 0.002 PHE A 378 TYR 0.007 0.002 TYR B 310 ARG 0.001 0.000 ARG B 349 *********************** 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 70 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.295 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.3366 time to fit residues: 23.8304 Evaluate side-chains 66 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1164 time to fit residues: 0.9069 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 16 optimal weight: 0.1980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** 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: 0.8522 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2166 Z= 0.242 Angle : 0.619 6.078 2892 Z= 0.295 Chirality : 0.050 0.121 321 Planarity : 0.004 0.034 369 Dihedral : 4.680 16.433 285 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.82 % Allowed : 22.22 % Favored : 76.95 % 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: -2.89 (0.40), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.005 0.001 PHE A 378 TYR 0.021 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** 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 73 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.272 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.3267 time to fit residues: 25.2280 Evaluate side-chains 68 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0497 time to fit residues: 0.4385 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 7 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 23 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 overall best weight: 0.2578 ------------------------------------------------------------------------------- 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: 0.8509 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2166 Z= 0.207 Angle : 0.610 6.071 2892 Z= 0.291 Chirality : 0.050 0.121 321 Planarity : 0.004 0.032 369 Dihedral : 4.470 16.923 285 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.65 % Allowed : 23.05 % Favored : 75.31 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE B 346 TYR 0.022 0.003 TYR B 310 ARG 0.000 0.000 ARG B 349 *********************** 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: 4 poor density : 72 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 72 average time/residue: 0.3430 time to fit residues: 26.4332 Evaluate side-chains 70 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0376 time to fit residues: 0.4809 ------------------------------------------------------------------------------- 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: 0.7980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8529 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2166 Z= 0.339 Angle : 0.682 6.490 2892 Z= 0.324 Chirality : 0.051 0.125 321 Planarity : 0.004 0.031 369 Dihedral : 4.702 16.331 285 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.82 % Allowed : 24.28 % Favored : 74.90 % 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: -2.76 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.008 0.001 PHE A 378 TYR 0.022 0.003 TYR B 310 ARG 0.001 0.000 ARG A 349 *********************** 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 66 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.252 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.3305 time to fit residues: 23.1019 Evaluate side-chains 64 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0253 time to fit residues: 0.4067 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8544 moved from start: 0.3948 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= 0.437 Angle : 0.730 7.840 2892 Z= 0.348 Chirality : 0.052 0.131 321 Planarity : 0.004 0.028 369 Dihedral : 4.998 16.967 285 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.06 % Allowed : 23.05 % Favored : 74.90 % 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: -2.76 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 330 PHE 0.010 0.002 PHE A 378 TYR 0.023 0.003 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** 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 71 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.3331 time to fit residues: 23.8753 Evaluate side-chains 69 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.258 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0399 time to fit residues: 0.5354 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** 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: 0.8536 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2166 Z= 0.369 Angle : 0.730 9.083 2892 Z= 0.347 Chirality : 0.052 0.123 321 Planarity : 0.004 0.029 369 Dihedral : 4.987 16.471 285 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.41 % Allowed : 24.69 % Favored : 74.90 % 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: -2.78 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.008 0.001 PHE A 378 TYR 0.024 0.003 TYR B 310 ARG 0.001 0.000 ARG C 349 ********************** 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 68 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.261 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.3261 time to fit residues: 23.4044 Evaluate side-chains 67 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3777 ------------------------------------------------------------------------------- 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: 0.0010 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.0030 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059578 restraints weight = 3598.439| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.48 r_work: 0.2819 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2166 Z= 0.291 Angle : 0.713 8.901 2892 Z= 0.337 Chirality : 0.051 0.123 321 Planarity : 0.004 0.030 369 Dihedral : 4.850 15.420 285 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.65 % Allowed : 24.28 % Favored : 74.07 % 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: -2.81 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.006 0.001 PHE A 378 TYR 0.023 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.65 seconds wall clock time: 24 minutes 4.41 seconds (1444.41 seconds total)