Starting phenix.real_space_refine on Sat Aug 3 05:02:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbm_44422/08_2024/9bbm_44422_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbm_44422/08_2024/9bbm_44422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbm_44422/08_2024/9bbm_44422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbm_44422/08_2024/9bbm_44422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbm_44422/08_2024/9bbm_44422_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbm_44422/08_2024/9bbm_44422_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2142 2.51 5 N 630 2.21 5 O 630 1.98 5 H 3558 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6966 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 4.71, per 1000 atoms: 0.68 Number of scatterers: 6966 At special positions: 0 Unit cell: (143.1, 78.44, 37.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 630 8.00 N 630 7.00 C 2142 6.00 H 3558 1.00 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: 5.47 Conformation dependent library (CDL) restraints added in 817.7 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.474A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.405A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.858A pdb=" N SER C 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS A 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY E 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER C 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.567A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.667A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS C 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 378 removed outlier: 6.594A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU C 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.080A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LYS F 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE D 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 354 Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.505A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS F 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 370 through 371 removed outlier: 6.213A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 375 through 378 Processing sheet with id=AC2, first strand: chain 'D' and resid 320 through 321 removed outlier: 6.577A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 48 hydrogen bonds defined for protein. 144 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: 2.05 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3552 1.12 - 1.30: 567 1.30 - 1.47: 1169 1.47 - 1.64: 1726 1.64 - 1.82: 6 Bond restraints: 7020 Sorted by residual: bond pdb=" NE2 HIS A 362 " pdb=" HE2 HIS A 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N GLN A 307 " pdb=" H GLN A 307 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N SER C 356 " pdb=" H SER C 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ILE F 308 " pdb=" H ILE F 308 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLU B 338 " pdb=" H GLU B 338 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 7015 not shown) Histogram of bond angle deviations from ideal: 96.70 - 103.47: 20 103.47 - 110.23: 6776 110.23 - 116.99: 2633 116.99 - 123.75: 2890 123.75 - 130.51: 479 Bond angle restraints: 12798 Sorted by residual: angle pdb=" CA PHE C 346 " pdb=" CB PHE C 346 " pdb=" CG PHE C 346 " ideal model delta sigma weight residual 113.80 120.08 -6.28 1.00e+00 1.00e+00 3.94e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.32 -5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 119.12 -5.32 1.00e+00 1.00e+00 2.84e+01 angle pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " pdb=" CG PHE A 346 " ideal model delta sigma weight residual 113.80 118.98 -5.18 1.00e+00 1.00e+00 2.68e+01 ... (remaining 12793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 2797 16.53 - 33.06: 248 33.06 - 49.59: 85 49.59 - 66.12: 91 66.12 - 82.66: 7 Dihedral angle restraints: 3228 sinusoidal: 1848 harmonic: 1380 Sorted by residual: dihedral pdb=" CA LEU B 325 " pdb=" C LEU B 325 " pdb=" N GLY B 326 " pdb=" CA GLY B 326 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LEU D 325 " pdb=" C LEU D 325 " pdb=" N GLY D 326 " pdb=" CA GLY D 326 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL E 339 " pdb=" C VAL E 339 " pdb=" N LYS E 340 " pdb=" CA LYS E 340 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 3225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 296 0.086 - 0.172: 172 0.172 - 0.258: 44 0.258 - 0.343: 5 0.343 - 0.429: 5 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA ASP C 348 " pdb=" N ASP C 348 " pdb=" C ASP C 348 " pdb=" CB ASP C 348 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA PRO C 364 " pdb=" N PRO C 364 " pdb=" C PRO C 364 " pdb=" CB PRO C 364 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA PRO E 364 " pdb=" N PRO E 364 " pdb=" C PRO E 364 " pdb=" CB PRO E 364 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 519 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.163 2.00e-02 2.50e+03 6.54e-02 1.28e+02 pdb=" CG TYR C 310 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.114 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.045 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 330 " -0.126 2.00e-02 2.50e+03 7.13e-02 1.14e+02 pdb=" CG HIS D 330 " 0.068 2.00e-02 2.50e+03 pdb=" ND1 HIS D 330 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 HIS D 330 " 0.074 2.00e-02 2.50e+03 pdb=" CE1 HIS D 330 " 0.030 2.00e-02 2.50e+03 pdb=" NE2 HIS D 330 " 0.046 2.00e-02 2.50e+03 pdb=" HD2 HIS D 330 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 HIS D 330 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 HIS D 330 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 330 " 0.116 2.00e-02 2.50e+03 6.51e-02 9.53e+01 pdb=" CG HIS C 330 " -0.076 2.00e-02 2.50e+03 pdb=" ND1 HIS C 330 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 HIS C 330 " -0.069 2.00e-02 2.50e+03 pdb=" CE1 HIS C 330 " -0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS C 330 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 HIS C 330 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 HIS C 330 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 HIS C 330 " 0.077 2.00e-02 2.50e+03 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 492 2.17 - 2.78: 11929 2.78 - 3.38: 18796 3.38 - 3.99: 24703 3.99 - 4.60: 35640 Nonbonded interactions: 91560 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.560 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.563 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.564 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.617 2.450 ... (remaining 91555 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.230 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: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.460 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 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 0.039 3462 Z= 0.773 Angle : 2.054 8.969 4632 Z= 1.328 Chirality : 0.109 0.429 522 Planarity : 0.013 0.105 588 Dihedral : 13.726 82.656 1332 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 4.86 % Allowed : 12.73 % Favored : 82.41 % Rotamer: Outliers : 0.51 % Allowed : 4.87 % Favored : 94.62 % Cbeta Deviations : 1.03 % 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: -3.91 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS C 362 PHE 0.041 0.011 PHE A 378 TYR 0.146 0.038 TYR C 310 ARG 0.006 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.5028 (mtt-85) cc_final: 0.4038 (ppt170) REVERT: C 342 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.5176 (mp0) REVERT: C 349 ARG cc_start: 0.5618 (mtt-85) cc_final: 0.5390 (mtt90) REVERT: C 369 LYS cc_start: 0.6313 (mttt) cc_final: 0.6011 (mtmm) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.6460 time to fit residues: 84.1847 Evaluate side-chains 62 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS C 336 GLN D 351 GLN E 336 GLN F 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3462 Z= 0.217 Angle : 0.751 6.039 4632 Z= 0.393 Chirality : 0.052 0.169 522 Planarity : 0.004 0.050 588 Dihedral : 8.308 43.418 459 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.93 % Allowed : 11.34 % Favored : 87.73 % Rotamer: Outliers : 1.54 % Allowed : 10.26 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 362 PHE 0.011 0.001 PHE C 378 TYR 0.018 0.004 TYR C 310 ARG 0.006 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.4899 (tp30) cc_final: 0.4603 (tp30) REVERT: A 349 ARG cc_start: 0.5226 (mtt180) cc_final: 0.4210 (ppt170) REVERT: B 371 ILE cc_start: 0.7632 (mt) cc_final: 0.7399 (mp) REVERT: C 342 GLU cc_start: 0.5369 (OUTLIER) cc_final: 0.4841 (mp0) REVERT: C 349 ARG cc_start: 0.5337 (mtt-85) cc_final: 0.5115 (mtt90) REVERT: E 311 LYS cc_start: 0.5955 (tppt) cc_final: 0.5723 (tppt) outliers start: 6 outliers final: 2 residues processed: 83 average time/residue: 0.6156 time to fit residues: 57.2568 Evaluate side-chains 65 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.0470 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3462 Z= 0.217 Angle : 0.660 5.390 4632 Z= 0.341 Chirality : 0.051 0.155 522 Planarity : 0.004 0.044 588 Dihedral : 7.346 45.206 459 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.93 % Allowed : 10.42 % Favored : 88.66 % Rotamer: Outliers : 1.79 % Allowed : 11.28 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 362 PHE 0.009 0.002 PHE D 378 TYR 0.021 0.004 TYR C 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 ILE cc_start: 0.7611 (mt) cc_final: 0.7403 (mp) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.5767 time to fit residues: 46.5525 Evaluate side-chains 57 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.6450 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3462 Z= 0.203 Angle : 0.607 4.728 4632 Z= 0.312 Chirality : 0.050 0.147 522 Planarity : 0.004 0.042 588 Dihedral : 6.983 47.763 459 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.95 % Favored : 89.12 % Rotamer: Outliers : 1.03 % Allowed : 12.82 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.009 0.002 PHE C 378 TYR 0.016 0.004 TYR C 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 ILE cc_start: 0.7624 (mt) cc_final: 0.7403 (mp) REVERT: D 351 GLN cc_start: 0.5514 (tt0) cc_final: 0.5296 (tt0) REVERT: E 370 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6913 (tttp) REVERT: E 375 LYS cc_start: 0.6945 (tttt) cc_final: 0.6742 (tttp) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.4753 time to fit residues: 34.8264 Evaluate side-chains 58 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 370 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.6491 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3462 Z= 0.245 Angle : 0.613 5.698 4632 Z= 0.317 Chirality : 0.050 0.146 522 Planarity : 0.004 0.042 588 Dihedral : 6.918 48.465 459 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.93 % Allowed : 11.81 % Favored : 87.27 % Rotamer: Outliers : 2.56 % Allowed : 12.31 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.010 0.002 PHE D 378 TYR 0.018 0.004 TYR E 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7818 (tt) REVERT: E 375 LYS cc_start: 0.6934 (tttt) cc_final: 0.6689 (tttp) outliers start: 10 outliers final: 4 residues processed: 61 average time/residue: 0.4651 time to fit residues: 33.2128 Evaluate side-chains 55 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.6485 moved from start: 0.7021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3462 Z= 0.202 Angle : 0.604 7.662 4632 Z= 0.305 Chirality : 0.050 0.147 522 Planarity : 0.004 0.043 588 Dihedral : 6.723 49.342 459 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.93 % Allowed : 10.42 % Favored : 88.66 % Rotamer: Outliers : 1.79 % Allowed : 14.10 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.007 0.001 PHE D 378 TYR 0.013 0.003 TYR C 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 375 LYS cc_start: 0.6971 (tttt) cc_final: 0.6749 (tttp) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.4847 time to fit residues: 33.1717 Evaluate side-chains 57 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.6525 moved from start: 0.7138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3462 Z= 0.281 Angle : 0.631 6.301 4632 Z= 0.325 Chirality : 0.050 0.147 522 Planarity : 0.004 0.041 588 Dihedral : 6.879 50.359 459 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.93 % Allowed : 11.57 % Favored : 87.50 % Rotamer: Outliers : 1.79 % Allowed : 14.10 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.011 0.002 PHE D 378 TYR 0.019 0.005 TYR A 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 375 LYS cc_start: 0.6999 (tttt) cc_final: 0.6767 (tttp) outliers start: 7 outliers final: 7 residues processed: 59 average time/residue: 0.4982 time to fit residues: 34.2723 Evaluate side-chains 57 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.6518 moved from start: 0.7287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3462 Z= 0.231 Angle : 0.608 6.224 4632 Z= 0.310 Chirality : 0.050 0.147 522 Planarity : 0.004 0.040 588 Dihedral : 6.742 51.121 459 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.93 % Allowed : 10.88 % Favored : 88.19 % Rotamer: Outliers : 1.54 % Allowed : 14.36 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.008 0.001 PHE D 378 TYR 0.015 0.004 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 371 ILE cc_start: 0.7589 (mt) cc_final: 0.7238 (mt) REVERT: E 375 LYS cc_start: 0.7046 (tttt) cc_final: 0.6804 (tttp) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.4509 time to fit residues: 30.4850 Evaluate side-chains 57 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3462 Z= 0.158 Angle : 0.560 6.175 4632 Z= 0.283 Chirality : 0.049 0.146 522 Planarity : 0.004 0.040 588 Dihedral : 6.389 52.617 459 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.49 % Favored : 89.58 % Rotamer: Outliers : 1.79 % Allowed : 14.10 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.008 0.001 PHE B 378 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 371 ILE cc_start: 0.7560 (mt) cc_final: 0.7187 (mt) REVERT: E 375 LYS cc_start: 0.7025 (tttt) cc_final: 0.6799 (tttp) REVERT: F 338 GLU cc_start: 0.4532 (mt-10) cc_final: 0.4282 (mt-10) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.4492 time to fit residues: 31.9133 Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.6440 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3462 Z= 0.148 Angle : 0.547 6.204 4632 Z= 0.275 Chirality : 0.049 0.141 522 Planarity : 0.004 0.040 588 Dihedral : 6.111 52.283 459 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.26 % Favored : 89.81 % Rotamer: Outliers : 1.28 % Allowed : 14.62 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.35), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.008 0.001 PHE B 378 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 338 GLU cc_start: 0.4993 (tp30) cc_final: 0.4703 (tp30) REVERT: E 375 LYS cc_start: 0.6992 (tttt) cc_final: 0.6773 (tttp) outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 0.4687 time to fit residues: 35.6857 Evaluate side-chains 62 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.158031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.148382 restraints weight = 15079.527| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.05 r_work: 0.4296 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4210 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3462 Z= 0.201 Angle : 0.570 6.013 4632 Z= 0.290 Chirality : 0.049 0.140 522 Planarity : 0.004 0.041 588 Dihedral : 6.289 53.112 459 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.93 % Allowed : 10.65 % Favored : 88.43 % Rotamer: Outliers : 1.54 % Allowed : 14.62 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.35), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.008 0.001 PHE D 378 TYR 0.014 0.003 TYR E 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.97 seconds wall clock time: 52 minutes 42.27 seconds (3162.27 seconds total)