Starting phenix.real_space_refine on Thu Dec 7 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/12_2023/6qjh_4563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/12_2023/6qjh_4563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/12_2023/6qjh_4563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/12_2023/6qjh_4563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/12_2023/6qjh_4563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/12_2023/6qjh_4563.pdb" } resolution = 3.3 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= 0.001 sd= 0.015 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 6 5.16 5 C 810 2.51 5 N 243 2.21 5 O 243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 1302 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 434 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "C" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 434 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "B" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 434 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Time building chain proxies: 1.11, per 1000 atoms: 0.85 Number of scatterers: 1302 At special positions: 0 Unit cell: (59.34, 99.36, 49.68, 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 6 16.00 O 243 8.00 N 243 7.00 C 810 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: 0.37 Conformation dependent library (CDL) restraints added in 238.6 milliseconds 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 306 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 44.1% 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 'C' and resid 275 through 291 removed outlier: 6.188A pdb=" N VAL A 275 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE C 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 277 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LYS C 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASN A 279 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU C 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS A 281 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N LEU C 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ASP A 283 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N ASN C 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N SER A 285 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N GLN C 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N VAL A 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N LYS C 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N SER A 289 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 282 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP B 283 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 284 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER B 285 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A 286 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B 287 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN A 288 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER B 289 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS A 290 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N CYS B 291 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 296 through 298 removed outlier: 6.359A pdb=" N ASN A 296 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.693A pdb=" N SER A 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ILE C 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314 removed outlier: 7.051A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.614A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 328 removed outlier: 6.513A pdb=" N ASN A 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) 16 hydrogen bonds defined for protein. 48 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: 0.24 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 321 1.34 - 1.46: 261 1.46 - 1.58: 729 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 1317 Sorted by residual: bond pdb=" C LYS C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.334 1.379 -0.045 1.11e-02 8.12e+03 1.65e+01 bond pdb=" C LYS A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 1.334 1.379 -0.045 1.11e-02 8.12e+03 1.65e+01 bond pdb=" C LYS B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.334 1.379 -0.045 1.11e-02 8.12e+03 1.62e+01 bond pdb=" C VAL B 300 " pdb=" N PRO B 301 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.25e-02 6.40e+03 1.19e+01 bond pdb=" C VAL A 300 " pdb=" N PRO A 301 " ideal model delta sigma weight residual 1.329 1.372 -0.042 1.25e-02 6.40e+03 1.15e+01 ... (remaining 1312 not shown) Histogram of bond angle deviations from ideal: 102.76 - 108.52: 108 108.52 - 114.27: 738 114.27 - 120.03: 315 120.03 - 125.79: 585 125.79 - 131.55: 15 Bond angle restraints: 1761 Sorted by residual: angle pdb=" CA LYS A 311 " pdb=" C LYS A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 118.16 121.34 -3.18 7.00e-01 2.04e+00 2.07e+01 angle pdb=" CA LYS C 311 " pdb=" C LYS C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 118.16 121.31 -3.15 7.00e-01 2.04e+00 2.02e+01 angle pdb=" CA LYS B 311 " pdb=" C LYS B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 118.16 121.30 -3.14 7.00e-01 2.04e+00 2.01e+01 angle pdb=" C TYR B 310 " pdb=" N LYS B 311 " pdb=" CA LYS B 311 " ideal model delta sigma weight residual 123.10 126.35 -3.25 9.60e-01 1.09e+00 1.14e+01 angle pdb=" C LYS B 281 " pdb=" CA LYS B 281 " pdb=" CB LYS B 281 " ideal model delta sigma weight residual 110.42 117.12 -6.70 1.99e+00 2.53e-01 1.13e+01 ... (remaining 1756 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 10.52: 630 10.52 - 21.02: 126 21.02 - 31.52: 24 31.52 - 42.01: 12 42.01 - 52.51: 15 Dihedral angle restraints: 807 sinusoidal: 324 harmonic: 483 Sorted by residual: dihedral pdb=" C LYS B 281 " pdb=" N LYS B 281 " pdb=" CA LYS B 281 " pdb=" CB LYS B 281 " ideal model delta harmonic sigma weight residual -122.60 -133.03 10.43 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" C LYS A 281 " pdb=" N LYS A 281 " pdb=" CA LYS A 281 " pdb=" CB LYS A 281 " ideal model delta harmonic sigma weight residual -122.60 -133.01 10.41 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" C LYS C 281 " pdb=" N LYS C 281 " pdb=" CA LYS C 281 " pdb=" CB LYS C 281 " ideal model delta harmonic sigma weight residual -122.60 -132.99 10.39 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 126 0.077 - 0.153: 67 0.153 - 0.229: 8 0.229 - 0.305: 0 0.305 - 0.381: 3 Chirality restraints: 204 Sorted by residual: chirality pdb=" CA LYS A 281 " pdb=" N LYS A 281 " pdb=" C LYS A 281 " pdb=" CB LYS A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA LYS B 281 " pdb=" N LYS B 281 " pdb=" C LYS B 281 " pdb=" CB LYS B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA LYS C 281 " pdb=" N LYS C 281 " pdb=" C LYS C 281 " pdb=" CB LYS C 281 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 201 not shown) Planarity restraints: 222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 321 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C LYS A 321 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 321 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS A 322 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 321 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C LYS B 321 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS B 321 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS B 322 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 321 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C LYS C 321 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS C 321 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS C 322 " -0.015 2.00e-02 2.50e+03 ... (remaining 219 not shown) Histogram of nonbonded interaction distances: 2.67 - 3.12: 828 3.12 - 3.56: 1250 3.56 - 4.01: 1878 4.01 - 4.45: 1792 4.45 - 4.90: 3861 Nonbonded interactions: 9609 Sorted by model distance: nonbonded pdb=" N LEU C 325 " pdb=" O LEU C 325 " model vdw 2.674 2.496 nonbonded pdb=" N LEU A 325 " pdb=" O LEU A 325 " model vdw 2.674 2.496 nonbonded pdb=" N LEU B 325 " pdb=" O LEU B 325 " model vdw 2.674 2.496 nonbonded pdb=" O VAL A 275 " pdb=" N GLN C 276 " model vdw 2.676 2.520 nonbonded pdb=" N LYS A 311 " pdb=" O TYR C 310 " model vdw 2.682 2.520 ... (remaining 9604 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: 0.950 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: 3.340 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.150 Find NCS groups from input model: 0.070 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.012 0.054 1317 Z= 0.810 Angle : 1.206 6.702 1761 Z= 0.777 Chirality : 0.096 0.381 204 Planarity : 0.010 0.039 222 Dihedral : 14.394 52.512 501 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.96 % Allowed : 11.76 % Favored : 86.27 % Cbeta Deviations : 1.96 % 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: -3.22 (0.46), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.35), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 299 TYR 0.011 0.004 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.164 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 41 average time/residue: 0.1678 time to fit residues: 7.6009 Evaluate side-chains 19 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 1317 Z= 0.242 Angle : 0.692 7.868 1761 Z= 0.342 Chirality : 0.054 0.126 204 Planarity : 0.004 0.030 222 Dihedral : 6.187 14.807 177 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.23 % Allowed : 18.30 % Favored : 76.47 % 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 (0.46), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.35), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.005 0.001 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 0.160 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 26 average time/residue: 0.1524 time to fit residues: 4.5155 Evaluate side-chains 24 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 17 time to evaluate : 0.162 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0179 time to fit residues: 0.4248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1317 Z= 0.240 Angle : 0.592 5.464 1761 Z= 0.299 Chirality : 0.052 0.138 204 Planarity : 0.004 0.029 222 Dihedral : 5.570 15.375 177 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.61 % Allowed : 18.30 % Favored : 79.08 % 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: -3.01 (0.49), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.37), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.006 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.167 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 25 average time/residue: 0.1302 time to fit residues: 3.7770 Evaluate side-chains 18 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.161 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0191 time to fit residues: 0.2631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1317 Z= 0.248 Angle : 0.563 4.784 1761 Z= 0.283 Chirality : 0.052 0.123 204 Planarity : 0.004 0.028 222 Dihedral : 5.349 14.264 177 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.92 % Allowed : 20.26 % Favored : 75.82 % 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: -3.02 (0.50), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.38), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 TYR 0.007 0.002 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.165 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.1301 time to fit residues: 3.6313 Evaluate side-chains 22 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.157 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0171 time to fit residues: 0.3019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1317 Z= 0.209 Angle : 0.542 5.107 1761 Z= 0.269 Chirality : 0.052 0.124 204 Planarity : 0.004 0.034 222 Dihedral : 5.061 14.319 177 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.61 % Allowed : 20.92 % Favored : 76.47 % 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: -2.86 (0.52), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 TYR 0.006 0.001 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.159 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.1634 time to fit residues: 4.6203 Evaluate side-chains 20 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.164 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0177 time to fit residues: 0.2871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1317 Z= 0.275 Angle : 0.583 8.413 1761 Z= 0.283 Chirality : 0.052 0.124 204 Planarity : 0.004 0.028 222 Dihedral : 5.083 13.939 177 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.65 % Allowed : 24.18 % Favored : 75.16 % 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 (0.53), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 TYR 0.008 0.002 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.162 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.2181 time to fit residues: 4.8536 Evaluate side-chains 20 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1317 Z= 0.242 Angle : 0.556 7.723 1761 Z= 0.272 Chirality : 0.052 0.123 204 Planarity : 0.004 0.032 222 Dihedral : 4.964 13.797 177 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.96 % Allowed : 23.53 % Favored : 74.51 % 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 (0.53), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 TYR 0.007 0.002 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.165 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 20 average time/residue: 0.2373 time to fit residues: 5.2209 Evaluate side-chains 23 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.142 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1178 time to fit residues: 0.6097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1317 Z= 0.214 Angle : 0.527 6.861 1761 Z= 0.260 Chirality : 0.052 0.122 204 Planarity : 0.003 0.027 222 Dihedral : 4.846 13.394 177 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 24.18 % Favored : 75.82 % 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: -2.81 (0.53), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 329 TYR 0.007 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.119 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1704 time to fit residues: 4.7270 Evaluate side-chains 22 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1317 Z= 0.238 Angle : 0.596 7.025 1761 Z= 0.280 Chirality : 0.053 0.123 204 Planarity : 0.004 0.028 222 Dihedral : 4.937 16.466 177 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.65 % Allowed : 26.14 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.53), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 TYR 0.007 0.002 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.161 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.2687 time to fit residues: 6.2676 Evaluate side-chains 21 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.224 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0224 time to fit residues: 0.3571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1317 Z= 0.174 Angle : 0.530 6.200 1761 Z= 0.253 Chirality : 0.052 0.122 204 Planarity : 0.003 0.026 222 Dihedral : 4.740 15.702 177 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 25.49 % Favored : 74.51 % 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: -2.70 (0.54), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 TYR 0.005 0.001 TYR B 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.161 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1853 time to fit residues: 4.7744 Evaluate side-chains 21 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.0030 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** 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 = 0.4431 r_free = 0.4431 target = 0.145229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.104441 restraints weight = 1601.739| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.51 r_work: 0.3885 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1317 Z= 0.179 Angle : 0.552 6.423 1761 Z= 0.257 Chirality : 0.052 0.120 204 Planarity : 0.003 0.027 222 Dihedral : 4.692 15.188 177 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 26.14 % Favored : 73.86 % 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: -2.63 (0.55), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 TYR 0.005 0.001 TYR B 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 885.66 seconds wall clock time: 21 minutes 26.09 seconds (1286.09 seconds total)