Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/03_2024/6qjh_4563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/03_2024/6qjh_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_4563/03_2024/6qjh_4563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/03_2024/6qjh_4563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/03_2024/6qjh_4563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/03_2024/6qjh_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.59, per 1000 atoms: 1.22 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: 0.41 Conformation dependent library (CDL) restraints added in 409.1 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: 0.18 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: 0.27 Time building geometry restraints manager: 0.45 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.360 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.120 Find NCS groups from input model: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- 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 : 0.160 Fit side-chains REVERT: A 295 ASP cc_start: 0.9033 (p0) cc_final: 0.8773 (p0) REVERT: C 290 LYS cc_start: 0.8542 (mttt) cc_final: 0.8281 (mmtp) REVERT: C 315 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8371 (tt) REVERT: B 294 LYS cc_start: 0.8118 (mttt) cc_final: 0.7503 (mptt) REVERT: B 295 ASP cc_start: 0.8598 (p0) cc_final: 0.7597 (m-30) outliers start: 3 outliers final: 0 residues processed: 41 average time/residue: 0.1882 time to fit residues: 8.4566 Evaluate side-chains 21 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1317 Z= 0.211 Angle : 0.606 6.003 1761 Z= 0.308 Chirality : 0.053 0.127 204 Planarity : 0.004 0.031 222 Dihedral : 6.954 42.578 179 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.58 % Allowed : 16.99 % Favored : 78.43 % 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: -2.98 (0.46), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.35), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.004 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 30 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.177 Fit side-chains REVERT: A 295 ASP cc_start: 0.9126 (p0) cc_final: 0.8866 (p0) REVERT: A 327 ASN cc_start: 0.8492 (m-40) cc_final: 0.8183 (m-40) REVERT: C 290 LYS cc_start: 0.8501 (mttt) cc_final: 0.8249 (mmtp) REVERT: C 315 LEU cc_start: 0.8596 (mt) cc_final: 0.8367 (mt) REVERT: B 295 ASP cc_start: 0.8741 (p0) cc_final: 0.7373 (m-30) outliers start: 7 outliers final: 6 residues processed: 27 average time/residue: 0.1489 time to fit residues: 4.5834 Evaluate side-chains 25 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 LEU 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: 6.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1317 Z= 0.240 Angle : 0.558 5.869 1761 Z= 0.289 Chirality : 0.052 0.123 204 Planarity : 0.004 0.030 222 Dihedral : 5.627 14.778 177 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.92 % Allowed : 18.95 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.49), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.37), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 TYR 0.007 0.002 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 30 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.166 Fit side-chains REVERT: A 295 ASP cc_start: 0.9043 (p0) cc_final: 0.8836 (p0) REVERT: A 327 ASN cc_start: 0.8577 (m-40) cc_final: 0.8295 (m-40) REVERT: C 290 LYS cc_start: 0.8489 (mttt) cc_final: 0.8232 (mmtp) REVERT: B 295 ASP cc_start: 0.8730 (p0) cc_final: 0.7226 (m-30) outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 0.1475 time to fit residues: 4.7179 Evaluate side-chains 26 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain B residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 14 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 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1317 Z= 0.207 Angle : 0.534 5.325 1761 Z= 0.270 Chirality : 0.052 0.125 204 Planarity : 0.004 0.031 222 Dihedral : 5.259 14.324 177 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.58 % Allowed : 18.95 % 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: -2.85 (0.50), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.38), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 TYR 0.006 0.001 TYR C 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 32 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.152 Fit side-chains REVERT: A 327 ASN cc_start: 0.8611 (m-40) cc_final: 0.8306 (m-40) REVERT: C 290 LYS cc_start: 0.8448 (mttt) cc_final: 0.8182 (mmtp) REVERT: C 314 ASP cc_start: 0.7452 (m-30) cc_final: 0.7020 (t0) REVERT: B 295 ASP cc_start: 0.8841 (p0) cc_final: 0.7392 (m-30) REVERT: B 315 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8498 (mt) outliers start: 7 outliers final: 3 residues processed: 30 average time/residue: 0.1433 time to fit residues: 4.8704 Evaluate side-chains 25 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 LEU 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: 1.9990 chunk 4 optimal weight: 0.0170 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3166 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= 0.197 Angle : 0.536 5.552 1761 Z= 0.264 Chirality : 0.052 0.123 204 Planarity : 0.004 0.033 222 Dihedral : 5.027 14.298 177 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.92 % Allowed : 19.61 % 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: -2.82 (0.51), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.39), 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 28 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.166 Fit side-chains REVERT: C 290 LYS cc_start: 0.8404 (mttt) cc_final: 0.8132 (mmtp) REVERT: C 299 HIS cc_start: 0.8102 (m90) cc_final: 0.7882 (m90) REVERT: C 314 ASP cc_start: 0.7302 (m-30) cc_final: 0.7008 (t0) REVERT: B 295 ASP cc_start: 0.8818 (p0) cc_final: 0.7333 (m-30) REVERT: B 315 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8485 (mt) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.1656 time to fit residues: 4.8570 Evaluate side-chains 25 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 327 ASN 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: 0.6980 chunk 2 optimal weight: 30.0000 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3327 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= 0.284 Angle : 0.555 5.019 1761 Z= 0.279 Chirality : 0.052 0.123 204 Planarity : 0.004 0.029 222 Dihedral : 5.134 13.955 177 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.58 % Allowed : 20.26 % 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: -2.85 (0.52), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (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 C 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 29 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.175 Fit side-chains REVERT: C 290 LYS cc_start: 0.8357 (mttt) cc_final: 0.8114 (mmtp) REVERT: C 314 ASP cc_start: 0.7296 (m-30) cc_final: 0.6959 (t0) REVERT: B 295 ASP cc_start: 0.8830 (p0) cc_final: 0.7335 (m-30) outliers start: 7 outliers final: 6 residues processed: 26 average time/residue: 0.1760 time to fit residues: 5.1464 Evaluate side-chains 24 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 327 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 14 optimal weight: 0.0980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1317 Z= 0.157 Angle : 0.503 4.682 1761 Z= 0.247 Chirality : 0.052 0.124 204 Planarity : 0.003 0.031 222 Dihedral : 4.787 13.895 177 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.27 % Allowed : 20.92 % 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: -2.83 (0.52), 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 0.001 0.000 HIS A 329 TYR 0.004 0.001 TYR C 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 26 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.181 Fit side-chains REVERT: A 327 ASN cc_start: 0.8633 (m-40) cc_final: 0.8293 (m-40) REVERT: B 295 ASP cc_start: 0.8819 (p0) cc_final: 0.7311 (m-30) outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 0.1671 time to fit residues: 4.5432 Evaluate side-chains 24 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 ASN 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: 4.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1317 Z= 0.150 Angle : 0.526 8.751 1761 Z= 0.246 Chirality : 0.052 0.122 204 Planarity : 0.003 0.027 222 Dihedral : 4.599 13.652 177 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: -2.67 (0.54), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 TYR 0.004 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 26 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.167 Fit side-chains REVERT: A 327 ASN cc_start: 0.8633 (m-40) cc_final: 0.8300 (m-40) REVERT: B 295 ASP cc_start: 0.8768 (p0) cc_final: 0.7220 (m-30) REVERT: B 298 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8250 (mtpt) REVERT: B 314 ASP cc_start: 0.7338 (m-30) cc_final: 0.6786 (t0) outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.1648 time to fit residues: 4.6709 Evaluate side-chains 24 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.0040 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1317 Z= 0.266 Angle : 0.594 9.283 1761 Z= 0.279 Chirality : 0.052 0.121 204 Planarity : 0.004 0.029 222 Dihedral : 4.824 14.406 177 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.27 % Allowed : 20.26 % 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: -2.67 (0.54), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 TYR 0.009 0.002 TYR C 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 24 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.162 Fit side-chains REVERT: A 327 ASN cc_start: 0.8659 (m-40) cc_final: 0.8339 (m-40) REVERT: C 290 LYS cc_start: 0.8289 (mttt) cc_final: 0.8016 (mmtp) REVERT: B 295 ASP cc_start: 0.8786 (p0) cc_final: 0.7236 (m-30) outliers start: 5 outliers final: 5 residues processed: 23 average time/residue: 0.1633 time to fit residues: 4.2489 Evaluate side-chains 24 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 327 ASN 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: 3.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3900 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= 0.153 Angle : 0.533 7.745 1761 Z= 0.247 Chirality : 0.052 0.123 204 Planarity : 0.003 0.028 222 Dihedral : 4.577 13.586 177 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.27 % Allowed : 21.57 % 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: -2.59 (0.54), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 TYR 0.004 0.001 TYR C 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 25 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.162 Fit side-chains REVERT: A 327 ASN cc_start: 0.8641 (m-40) cc_final: 0.8306 (m-40) REVERT: B 295 ASP cc_start: 0.8764 (p0) cc_final: 0.7202 (m-30) REVERT: B 314 ASP cc_start: 0.7458 (m-30) cc_final: 0.6868 (t0) outliers start: 5 outliers final: 5 residues processed: 24 average time/residue: 0.1414 time to fit residues: 3.9078 Evaluate side-chains 24 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 327 ASN 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: 0.6980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.146116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.103481 restraints weight = 1626.727| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.55 r_work: 0.3812 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1317 Z= 0.208 Angle : 0.538 8.346 1761 Z= 0.256 Chirality : 0.052 0.120 204 Planarity : 0.003 0.027 222 Dihedral : 4.658 13.522 177 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.27 % Allowed : 20.92 % 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: -2.61 (0.54), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 TYR 0.006 0.001 TYR C 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 890.19 seconds wall clock time: 17 minutes 27.91 seconds (1047.91 seconds total)