Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/09_2024/6qjh_4563.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/09_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_4563/09_2024/6qjh_4563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/09_2024/6qjh_4563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/09_2024/6qjh_4563.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjh_4563/09_2024/6qjh_4563.cif" } 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. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1302 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B Time building chain proxies: 0.95, per 1000 atoms: 0.73 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 524.8 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: 0.20 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: 0.38 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: 0.00 - 1.34: 1401 1.34 - 2.68: 282 2.68 - 4.02: 69 4.02 - 5.36: 6 5.36 - 6.70: 3 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 3.120 nonbonded pdb=" N LYS A 311 " pdb=" O TYR C 310 " model vdw 2.682 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.860 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.430 ------------------------------------------------------------------------------- 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 : 0.154 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: 0.1637 time to fit residues: 7.4149 Evaluate side-chains 21 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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: 7.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7975 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1317 Z= 0.215 Angle : 0.603 6.088 1761 Z= 0.309 Chirality : 0.053 0.125 204 Planarity : 0.004 0.032 222 Dihedral : 6.978 41.270 179 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.58 % Allowed : 15.69 % Favored : 79.74 % 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: -2.90 (0.47), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.36), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 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 34 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.158 Fit side-chains REVERT: A 295 ASP cc_start: 0.9054 (p0) cc_final: 0.8776 (p0) REVERT: A 327 ASN cc_start: 0.8477 (m-40) cc_final: 0.8206 (m-40) REVERT: C 290 LYS cc_start: 0.8432 (mttt) cc_final: 0.8187 (mmtp) REVERT: C 295 ASP cc_start: 0.8927 (p0) cc_final: 0.8548 (p0) REVERT: B 295 ASP cc_start: 0.8765 (p0) cc_final: 0.7453 (m-30) outliers start: 7 outliers final: 6 residues processed: 32 average time/residue: 0.1401 time to fit residues: 5.0812 Evaluate side-chains 27 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 C residue 319 THR 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: 4.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 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 ** 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: 0.7963 moved from start: 0.2785 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= 0.201 Angle : 0.571 5.864 1761 Z= 0.286 Chirality : 0.053 0.126 204 Planarity : 0.004 0.030 222 Dihedral : 5.468 14.777 177 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.58 % Allowed : 17.65 % Favored : 77.78 % 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 (0.49), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.37), 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 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 31 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.157 Fit side-chains REVERT: A 295 ASP cc_start: 0.9034 (p0) cc_final: 0.8769 (p0) REVERT: A 315 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8465 (tt) REVERT: A 327 ASN cc_start: 0.8604 (m-40) cc_final: 0.8305 (m-40) REVERT: C 290 LYS cc_start: 0.8361 (mttt) cc_final: 0.8100 (mmtp) REVERT: C 314 ASP cc_start: 0.7471 (m-30) cc_final: 0.6944 (t0) REVERT: B 295 ASP cc_start: 0.8778 (p0) cc_final: 0.7388 (m-30) outliers start: 7 outliers final: 4 residues processed: 29 average time/residue: 0.1485 time to fit residues: 4.8874 Evaluate side-chains 26 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 319 THR 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: 2.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.2931 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= 0.274 Angle : 0.574 5.110 1761 Z= 0.294 Chirality : 0.053 0.147 204 Planarity : 0.004 0.032 222 Dihedral : 5.330 14.437 177 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.27 % Allowed : 18.95 % Favored : 77.78 % 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 (0.50), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.38), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.009 0.002 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 26 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.148 Fit side-chains REVERT: A 295 ASP cc_start: 0.9027 (p0) cc_final: 0.8713 (p0) REVERT: A 327 ASN cc_start: 0.8640 (m-40) cc_final: 0.8281 (m-40) REVERT: C 314 ASP cc_start: 0.7318 (m-30) cc_final: 0.6881 (t0) REVERT: B 295 ASP cc_start: 0.8744 (p0) cc_final: 0.7282 (m-30) REVERT: B 315 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8572 (mt) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.1442 time to fit residues: 4.1610 Evaluate side-chains 23 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 B 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3170 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= 0.172 Angle : 0.508 4.521 1761 Z= 0.260 Chirality : 0.052 0.124 204 Planarity : 0.004 0.032 222 Dihedral : 4.934 14.249 177 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.27 % Allowed : 18.95 % Favored : 77.78 % 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: -2.69 (0.52), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.40), 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 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: 5 poor density : 22 time to evaluate : 0.167 Fit side-chains REVERT: A 295 ASP cc_start: 0.8958 (p0) cc_final: 0.8750 (p0) REVERT: A 327 ASN cc_start: 0.8651 (m-40) cc_final: 0.8245 (m-40) REVERT: C 314 ASP cc_start: 0.7169 (m-30) cc_final: 0.6934 (t0) REVERT: B 295 ASP cc_start: 0.8615 (p0) cc_final: 0.6971 (m-30) outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.1423 time to fit residues: 4.4115 Evaluate side-chains 25 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 288 GLN Chi-restraints excluded: chain B residue 305 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 12 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1317 Z= 0.195 Angle : 0.561 8.796 1761 Z= 0.274 Chirality : 0.052 0.125 204 Planarity : 0.004 0.030 222 Dihedral : 4.870 13.978 177 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.96 % Allowed : 18.95 % 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: -2.66 (0.52), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.006 0.001 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 25 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.155 Fit side-chains REVERT: A 295 ASP cc_start: 0.8949 (p0) cc_final: 0.8728 (p0) REVERT: A 327 ASN cc_start: 0.8650 (m-40) cc_final: 0.8249 (m-40) REVERT: C 299 HIS cc_start: 0.8076 (m90) cc_final: 0.7874 (m90) REVERT: B 293 SER cc_start: 0.7973 (p) cc_final: 0.7733 (p) REVERT: B 295 ASP cc_start: 0.8619 (p0) cc_final: 0.7126 (m-30) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.1398 time to fit residues: 4.0148 Evaluate side-chains 24 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1317 Z= 0.194 Angle : 0.550 8.449 1761 Z= 0.269 Chirality : 0.053 0.130 204 Planarity : 0.004 0.030 222 Dihedral : 4.863 13.925 177 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.96 % Allowed : 18.95 % 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: -2.56 (0.54), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.006 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 25 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.158 Fit side-chains REVERT: A 295 ASP cc_start: 0.8814 (p0) cc_final: 0.8530 (p0) REVERT: A 327 ASN cc_start: 0.8646 (m-40) cc_final: 0.8266 (m-40) REVERT: C 299 HIS cc_start: 0.8016 (m90) cc_final: 0.7801 (m90) REVERT: B 293 SER cc_start: 0.7989 (p) cc_final: 0.7750 (p) REVERT: B 295 ASP cc_start: 0.8581 (p0) cc_final: 0.7082 (m-30) REVERT: B 314 ASP cc_start: 0.7527 (m-30) cc_final: 0.6862 (t0) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.1418 time to fit residues: 4.0670 Evaluate side-chains 23 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 1317 Z= 0.217 Angle : 0.549 7.705 1761 Z= 0.272 Chirality : 0.053 0.136 204 Planarity : 0.004 0.030 222 Dihedral : 4.889 14.628 177 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.96 % Allowed : 18.95 % 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: -2.50 (0.54), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.007 0.001 TYR C 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 24 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.154 Fit side-chains REVERT: A 295 ASP cc_start: 0.8788 (p0) cc_final: 0.8495 (p0) REVERT: A 327 ASN cc_start: 0.8658 (m-40) cc_final: 0.8302 (m-40) REVERT: B 293 SER cc_start: 0.8003 (p) cc_final: 0.7763 (p) REVERT: B 295 ASP cc_start: 0.8646 (p0) cc_final: 0.7040 (m-30) REVERT: B 314 ASP cc_start: 0.7467 (m-30) cc_final: 0.6884 (t0) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1249 time to fit residues: 3.4983 Evaluate side-chains 23 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 1317 Z= 0.382 Angle : 0.628 8.322 1761 Z= 0.316 Chirality : 0.054 0.128 204 Planarity : 0.004 0.029 222 Dihedral : 5.155 13.365 177 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.96 % Allowed : 18.95 % 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: -2.63 (0.53), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 TYR 0.012 0.003 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: 3 poor density : 21 time to evaluate : 0.162 Fit side-chains REVERT: A 295 ASP cc_start: 0.8797 (p0) cc_final: 0.8515 (p0) REVERT: A 327 ASN cc_start: 0.8688 (m-40) cc_final: 0.8359 (m-40) REVERT: B 293 SER cc_start: 0.8024 (p) cc_final: 0.7785 (p) REVERT: B 295 ASP cc_start: 0.8608 (p0) cc_final: 0.7091 (m-30) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1736 time to fit residues: 4.6950 Evaluate side-chains 23 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1317 Z= 0.209 Angle : 0.555 7.220 1761 Z= 0.275 Chirality : 0.053 0.126 204 Planarity : 0.004 0.031 222 Dihedral : 4.912 13.662 177 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.96 % Allowed : 19.61 % 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: -2.55 (0.55), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 TYR 0.007 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 23 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.172 Fit side-chains REVERT: A 295 ASP cc_start: 0.8776 (p0) cc_final: 0.8479 (p0) REVERT: A 327 ASN cc_start: 0.8687 (m-40) cc_final: 0.8367 (m-40) REVERT: B 293 SER cc_start: 0.8034 (p) cc_final: 0.7791 (p) REVERT: B 295 ASP cc_start: 0.8483 (p0) cc_final: 0.6866 (m-30) REVERT: B 314 ASP cc_start: 0.7481 (m-30) cc_final: 0.6908 (t0) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1545 time to fit residues: 4.0950 Evaluate side-chains 23 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 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: 0.0060 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.0020 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.153505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.110588 restraints weight = 1574.156| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 3.59 r_work: 0.3941 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1317 Z= 0.158 Angle : 0.515 6.172 1761 Z= 0.254 Chirality : 0.053 0.124 204 Planarity : 0.003 0.028 222 Dihedral : 4.573 13.659 177 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.96 % Allowed : 19.61 % 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: -2.45 (0.56), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 299 TYR 0.004 0.001 TYR C 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 902.08 seconds wall clock time: 16 minutes 33.06 seconds (993.06 seconds total)