Starting phenix.real_space_refine on Sun Apr 7 23:45:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk3_14753/04_2024/7zk3_14753_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk3_14753/04_2024/7zk3_14753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk3_14753/04_2024/7zk3_14753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk3_14753/04_2024/7zk3_14753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk3_14753/04_2024/7zk3_14753_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk3_14753/04_2024/7zk3_14753_trim_updated.pdb" } resolution = 2.85 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 74 5.16 5 C 7770 2.51 5 N 1962 2.21 5 O 2080 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A TYR 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 883": "OD1" <-> "OD2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B TYR 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 883": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5926 Classifications: {'peptide': 721} Link IDs: {'PTRANS': 31, 'TRANS': 689} Chain breaks: 5 Chain: "B" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5926 Classifications: {'peptide': 721} Link IDs: {'PTRANS': 31, 'TRANS': 689} Chain breaks: 5 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 23 Unusual residues: {' CA': 3, 'JRF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 23 Unusual residues: {' CA': 3, 'JRF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.07, per 1000 atoms: 0.59 Number of scatterers: 11898 At special positions: 0 Unit cell: (91.977, 123.625, 114.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 74 16.00 F 6 9.00 O 2080 8.00 N 1962 7.00 C 7770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.03 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: 4.45 Conformation dependent library (CDL) restraints added in 2.1 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 4 sheets defined 61.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.669A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 203 through 210 Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 268 through 274 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 326 through 362 Proline residue: A 344 - end of helix removed outlier: 4.662A pdb=" N ASP A 361 " --> pdb=" O CYS A 357 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.507A pdb=" N ALA A 394 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA A 396 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 438 Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 487 through 524 Processing helix chain 'A' and resid 529 through 532 No H-bonds generated for 'chain 'A' and resid 529 through 532' Processing helix chain 'A' and resid 534 through 568 Processing helix chain 'A' and resid 573 through 601 Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 630 through 643 Processing helix chain 'A' and resid 649 through 667 Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 686 through 692 Processing helix chain 'A' and resid 700 through 715 Processing helix chain 'A' and resid 723 through 744 removed outlier: 4.063A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 removed outlier: 3.802A pdb=" N PHE A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 794 Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 814 through 816 No H-bonds generated for 'chain 'A' and resid 814 through 816' Processing helix chain 'A' and resid 855 through 885 Processing helix chain 'A' and resid 891 through 909 Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.669A pdb=" N LYS B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 203 through 210 Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 243 through 256 Processing helix chain 'B' and resid 268 through 274 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 326 through 362 Proline residue: B 344 - end of helix removed outlier: 4.661A pdb=" N ASP B 361 " --> pdb=" O CYS B 357 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 391 through 403 removed outlier: 3.507A pdb=" N ALA B 394 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA B 396 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 438 Processing helix chain 'B' and resid 453 through 465 Processing helix chain 'B' and resid 487 through 524 Processing helix chain 'B' and resid 529 through 532 No H-bonds generated for 'chain 'B' and resid 529 through 532' Processing helix chain 'B' and resid 534 through 568 Processing helix chain 'B' and resid 573 through 601 Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 630 through 643 Processing helix chain 'B' and resid 649 through 667 Proline residue: B 658 - end of helix Processing helix chain 'B' and resid 686 through 692 Processing helix chain 'B' and resid 700 through 715 Processing helix chain 'B' and resid 723 through 744 removed outlier: 4.065A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 781 removed outlier: 3.803A pdb=" N PHE B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 794 Processing helix chain 'B' and resid 804 through 808 Processing helix chain 'B' and resid 814 through 816 No H-bonds generated for 'chain 'B' and resid 814 through 816' Processing helix chain 'B' and resid 855 through 885 Processing helix chain 'B' and resid 891 through 909 Processing sheet with id= A, first strand: chain 'A' and resid 279 through 281 removed outlier: 3.524A pdb=" N ASP A 123 " --> pdb=" O GLN A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 810 through 813 Processing sheet with id= C, first strand: chain 'B' and resid 279 through 281 removed outlier: 3.524A pdb=" N ASP B 123 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 810 through 813 662 hydrogen bonds defined for protein. 1794 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: 3.57 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1858 1.29 - 1.43: 3376 1.43 - 1.56: 6840 1.56 - 1.70: 2 1.70 - 1.83: 122 Bond restraints: 12198 Sorted by residual: bond pdb=" C08 JRF B1003 " pdb=" C09 JRF B1003 " ideal model delta sigma weight residual 1.418 1.515 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C08 JRF A1003 " pdb=" C09 JRF A1003 " ideal model delta sigma weight residual 1.418 1.515 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C13 JRF A1003 " pdb=" N06 JRF A1003 " ideal model delta sigma weight residual 1.367 1.440 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C13 JRF B1003 " pdb=" N06 JRF B1003 " ideal model delta sigma weight residual 1.367 1.439 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C08 JRF B1003 " pdb=" N05 JRF B1003 " ideal model delta sigma weight residual 1.401 1.471 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 12193 not shown) Histogram of bond angle deviations from ideal: 100.02 - 116.00: 7734 116.00 - 131.98: 8741 131.98 - 147.97: 29 147.97 - 163.95: 0 163.95 - 179.93: 2 Bond angle restraints: 16506 Sorted by residual: angle pdb=" CA GLU A 186 " pdb=" CB GLU A 186 " pdb=" CG GLU A 186 " ideal model delta sigma weight residual 114.10 128.93 -14.83 2.00e+00 2.50e-01 5.50e+01 angle pdb=" CA GLU B 186 " pdb=" CB GLU B 186 " pdb=" CG GLU B 186 " ideal model delta sigma weight residual 114.10 128.91 -14.81 2.00e+00 2.50e-01 5.48e+01 angle pdb=" CB MET B 424 " pdb=" CG MET B 424 " pdb=" SD MET B 424 " ideal model delta sigma weight residual 112.70 127.13 -14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" CB MET A 424 " pdb=" CG MET A 424 " pdb=" SD MET A 424 " ideal model delta sigma weight residual 112.70 127.08 -14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" CB GLU B 186 " pdb=" CG GLU B 186 " pdb=" CD GLU B 186 " ideal model delta sigma weight residual 112.60 120.73 -8.13 1.70e+00 3.46e-01 2.29e+01 ... (remaining 16501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 6586 16.14 - 32.28: 533 32.28 - 48.42: 97 48.42 - 64.56: 52 64.56 - 80.70: 12 Dihedral angle restraints: 7280 sinusoidal: 3012 harmonic: 4268 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual -86.00 -166.70 80.70 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual -86.00 -166.68 80.68 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CA ARG B 621 " pdb=" C ARG B 621 " pdb=" N MET B 622 " pdb=" CA MET B 622 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 7277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1162 0.027 - 0.054: 380 0.054 - 0.081: 173 0.081 - 0.108: 79 0.108 - 0.135: 8 Chirality restraints: 1802 Sorted by residual: chirality pdb=" CA MET B 622 " pdb=" N MET B 622 " pdb=" C MET B 622 " pdb=" CB MET B 622 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA MET A 622 " pdb=" N MET A 622 " pdb=" C MET A 622 " pdb=" CB MET A 622 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 889 " pdb=" N ILE A 889 " pdb=" C ILE A 889 " pdb=" CB ILE A 889 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 1799 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 314 " 0.017 2.00e-02 2.50e+03 1.39e-02 3.89e+00 pdb=" CG TYR A 314 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 314 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 314 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 314 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 314 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 314 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 314 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 314 " 0.017 2.00e-02 2.50e+03 1.39e-02 3.89e+00 pdb=" CG TYR B 314 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 314 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 314 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 314 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 314 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 314 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 314 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 786 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 787 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 787 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 787 " 0.021 5.00e-02 4.00e+02 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 174 2.67 - 3.23: 11892 3.23 - 3.79: 18815 3.79 - 4.34: 24897 4.34 - 4.90: 41371 Nonbonded interactions: 97149 Sorted by model distance: nonbonded pdb=" N GLU A 186 " pdb=" OE1 GLU A 186 " model vdw 2.118 2.520 nonbonded pdb=" N GLU B 186 " pdb=" OE1 GLU B 186 " model vdw 2.119 2.520 nonbonded pdb=" OE1 GLN A 215 " pdb=" NH2 ARG A 753 " model vdw 2.232 2.520 nonbonded pdb=" OE1 GLN B 215 " pdb=" NH2 ARG B 753 " model vdw 2.233 2.520 nonbonded pdb=" O ASN A 406 " pdb=" OG1 THR A 409 " model vdw 2.284 2.440 ... (remaining 97144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 13.200 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 33.420 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.003 0.097 12198 Z= 0.191 Angle : 0.585 14.826 16506 Z= 0.286 Chirality : 0.036 0.135 1802 Planarity : 0.003 0.037 2060 Dihedral : 13.318 75.641 4492 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.09 % Allowed : 0.78 % Favored : 98.13 % 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: 1.70 (0.22), residues: 1418 helix: 2.63 (0.16), residues: 898 sheet: -0.61 (0.71), residues: 58 loop : -1.85 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 427 HIS 0.004 0.001 HIS B 402 PHE 0.008 0.001 PHE A 585 TYR 0.034 0.001 TYR A 314 ARG 0.006 0.000 ARG B 562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 1.335 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 212 average time/residue: 1.3947 time to fit residues: 318.0088 Evaluate side-chains 143 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 215 GLN A 229 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 493 ASN B 591 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12198 Z= 0.257 Angle : 0.579 9.571 16506 Z= 0.301 Chirality : 0.040 0.139 1802 Planarity : 0.005 0.032 2060 Dihedral : 4.072 22.836 1612 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.02 % Allowed : 8.79 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1418 helix: 2.35 (0.16), residues: 890 sheet: -1.15 (0.77), residues: 38 loop : -1.67 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.006 0.001 HIS A 898 PHE 0.015 0.001 PHE B 585 TYR 0.019 0.001 TYR A 514 ARG 0.004 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 276 VAL cc_start: 0.7308 (OUTLIER) cc_final: 0.7038 (m) REVERT: A 497 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7262 (mt) REVERT: A 889 ILE cc_start: 0.8074 (pp) cc_final: 0.7862 (mt) REVERT: B 497 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7347 (mt) REVERT: B 573 GLU cc_start: 0.6575 (mm-30) cc_final: 0.6318 (mm-30) REVERT: B 753 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6972 (ttp-170) REVERT: B 904 MET cc_start: 0.6913 (mmp) cc_final: 0.6633 (mmp) outliers start: 26 outliers final: 10 residues processed: 171 average time/residue: 1.4465 time to fit residues: 266.0752 Evaluate side-chains 161 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 131 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 898 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12198 Z= 0.246 Angle : 0.556 9.484 16506 Z= 0.289 Chirality : 0.040 0.143 1802 Planarity : 0.005 0.059 2060 Dihedral : 4.021 20.699 1612 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.49 % Allowed : 9.80 % Favored : 87.71 % 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: 1.13 (0.22), residues: 1418 helix: 2.06 (0.16), residues: 898 sheet: -0.80 (0.96), residues: 28 loop : -1.76 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.009 0.001 HIS A 898 PHE 0.022 0.001 PHE B 691 TYR 0.011 0.001 TYR B 687 ARG 0.005 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: A 276 VAL cc_start: 0.7255 (OUTLIER) cc_final: 0.6986 (m) REVERT: A 497 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7242 (mt) REVERT: B 256 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6179 (tmm160) REVERT: B 497 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7408 (mt) REVERT: B 753 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7147 (ttp-170) outliers start: 32 outliers final: 14 residues processed: 169 average time/residue: 1.4258 time to fit residues: 259.8494 Evaluate side-chains 158 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 843 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 139 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 0.0970 chunk 37 optimal weight: 0.3980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 898 HIS B 199 GLN B 591 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12198 Z= 0.177 Angle : 0.524 11.158 16506 Z= 0.270 Chirality : 0.038 0.144 1802 Planarity : 0.004 0.058 2060 Dihedral : 3.955 20.701 1612 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.57 % Allowed : 10.50 % Favored : 86.94 % 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: 1.12 (0.22), residues: 1418 helix: 2.11 (0.16), residues: 898 sheet: -0.90 (0.71), residues: 48 loop : -1.90 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.008 0.001 HIS A 898 PHE 0.013 0.001 PHE A 505 TYR 0.010 0.001 TYR B 687 ARG 0.006 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: A 206 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: A 276 VAL cc_start: 0.7062 (OUTLIER) cc_final: 0.6834 (m) REVERT: A 497 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7264 (mt) REVERT: A 753 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6126 (tmt90) REVERT: B 186 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: B 904 MET cc_start: 0.6916 (mmp) cc_final: 0.6686 (mmp) outliers start: 33 outliers final: 11 residues processed: 163 average time/residue: 1.3969 time to fit residues: 245.3914 Evaluate side-chains 156 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.5980 chunk 79 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 124 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12198 Z= 0.290 Angle : 0.578 8.883 16506 Z= 0.300 Chirality : 0.040 0.134 1802 Planarity : 0.005 0.074 2060 Dihedral : 4.131 21.262 1612 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.11 % Allowed : 11.51 % Favored : 85.38 % 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: 1.12 (0.22), residues: 1418 helix: 2.04 (0.17), residues: 892 sheet: -0.61 (1.01), residues: 28 loop : -1.70 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.009 0.001 HIS A 898 PHE 0.017 0.002 PHE A 585 TYR 0.011 0.001 TYR B 687 ARG 0.006 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 276 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6742 (m) REVERT: A 497 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7296 (mt) REVERT: A 500 MET cc_start: 0.6412 (mtt) cc_final: 0.5805 (mtt) REVERT: A 753 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6020 (tmt90) REVERT: A 769 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7824 (pttm) REVERT: B 126 PHE cc_start: 0.4957 (OUTLIER) cc_final: 0.4360 (t80) REVERT: B 186 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: B 226 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6646 (tmm160) REVERT: B 256 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7164 (ttm170) REVERT: B 753 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7278 (tmt170) REVERT: B 904 MET cc_start: 0.6930 (mmp) cc_final: 0.6653 (mmp) outliers start: 40 outliers final: 14 residues processed: 168 average time/residue: 1.4182 time to fit residues: 256.7397 Evaluate side-chains 168 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 0.0030 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 898 HIS B 493 ASN B 591 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12198 Z= 0.210 Angle : 0.574 17.069 16506 Z= 0.291 Chirality : 0.039 0.262 1802 Planarity : 0.005 0.088 2060 Dihedral : 4.124 24.287 1612 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.11 % Allowed : 12.21 % Favored : 84.68 % 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: 1.02 (0.22), residues: 1418 helix: 2.05 (0.17), residues: 894 sheet: -0.91 (0.75), residues: 48 loop : -1.96 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 427 HIS 0.009 0.001 HIS A 898 PHE 0.024 0.001 PHE A 126 TYR 0.011 0.001 TYR A 687 ARG 0.009 0.000 ARG B 461 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: A 206 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8073 (mp10) REVERT: A 497 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7293 (mt) REVERT: A 500 MET cc_start: 0.6613 (mtt) cc_final: 0.6088 (mtt) REVERT: A 578 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6187 (tt0) REVERT: A 753 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.5751 (tmt90) REVERT: B 126 PHE cc_start: 0.4821 (OUTLIER) cc_final: 0.4407 (t80) REVERT: B 186 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: B 226 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6659 (tmm160) REVERT: B 256 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7116 (ttm170) REVERT: B 753 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.5771 (tmt90) REVERT: B 904 MET cc_start: 0.6961 (mmp) cc_final: 0.6683 (mmp) outliers start: 40 outliers final: 15 residues processed: 170 average time/residue: 1.4363 time to fit residues: 262.8182 Evaluate side-chains 165 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0570 chunk 79 optimal weight: 0.1980 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 117 optimal weight: 0.0040 chunk 77 optimal weight: 0.0970 chunk 138 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.1508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS A 898 HIS B 493 ASN B 591 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 12198 Z= 0.149 Angle : 0.543 12.751 16506 Z= 0.275 Chirality : 0.038 0.133 1802 Planarity : 0.005 0.072 2060 Dihedral : 4.126 28.889 1612 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.33 % Allowed : 13.22 % Favored : 84.45 % 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: 1.27 (0.22), residues: 1418 helix: 2.26 (0.17), residues: 884 sheet: -0.86 (0.73), residues: 48 loop : -1.79 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 427 HIS 0.009 0.001 HIS A 898 PHE 0.011 0.001 PHE A 785 TYR 0.010 0.001 TYR A 687 ARG 0.011 0.000 ARG B 461 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: A 206 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: A 497 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7248 (mt) REVERT: A 500 MET cc_start: 0.6418 (mtt) cc_final: 0.5903 (mtt) REVERT: A 753 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7255 (tmm160) REVERT: B 126 PHE cc_start: 0.4904 (OUTLIER) cc_final: 0.4519 (t80) REVERT: B 186 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: B 194 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6197 (pp) REVERT: B 226 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6529 (tmm160) REVERT: B 256 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7119 (ttm170) REVERT: B 753 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7104 (ttp-170) REVERT: B 794 MET cc_start: 0.7832 (ttp) cc_final: 0.7612 (mtp) REVERT: B 904 MET cc_start: 0.7003 (mmp) cc_final: 0.6782 (mmp) outliers start: 30 outliers final: 13 residues processed: 165 average time/residue: 1.3855 time to fit residues: 246.9679 Evaluate side-chains 164 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 493 ASN B 591 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12198 Z= 0.324 Angle : 0.618 11.241 16506 Z= 0.315 Chirality : 0.041 0.144 1802 Planarity : 0.005 0.078 2060 Dihedral : 4.163 22.319 1612 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.64 % Allowed : 13.30 % Favored : 84.06 % 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: 1.03 (0.22), residues: 1418 helix: 2.06 (0.16), residues: 890 sheet: -1.09 (0.72), residues: 48 loop : -1.90 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 427 HIS 0.009 0.001 HIS A 898 PHE 0.018 0.002 PHE B 585 TYR 0.011 0.001 TYR B 598 ARG 0.010 0.001 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: A 497 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7321 (mt) REVERT: A 500 MET cc_start: 0.6661 (mtt) cc_final: 0.6212 (mtt) REVERT: B 126 PHE cc_start: 0.4998 (OUTLIER) cc_final: 0.4317 (t80) REVERT: B 186 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: B 226 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6693 (tmm160) REVERT: B 256 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7185 (ttm170) REVERT: B 497 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7344 (mt) REVERT: B 753 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7417 (tmt170) REVERT: B 904 MET cc_start: 0.7020 (mmp) cc_final: 0.6817 (mmp) outliers start: 34 outliers final: 16 residues processed: 164 average time/residue: 1.3608 time to fit residues: 241.1657 Evaluate side-chains 164 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.0270 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 122 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12198 Z= 0.190 Angle : 0.595 11.870 16506 Z= 0.299 Chirality : 0.039 0.174 1802 Planarity : 0.005 0.083 2060 Dihedral : 4.125 22.693 1612 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.94 % Allowed : 14.23 % Favored : 83.83 % 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: 1.16 (0.22), residues: 1418 helix: 2.20 (0.17), residues: 880 sheet: -0.96 (0.73), residues: 48 loop : -1.84 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 PHE 0.020 0.001 PHE A 126 TYR 0.010 0.001 TYR A 687 ARG 0.011 0.000 ARG B 461 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: A 497 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7298 (mt) REVERT: A 500 MET cc_start: 0.6450 (mtt) cc_final: 0.6010 (mtt) REVERT: A 578 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6176 (tt0) REVERT: A 753 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.5698 (tmt90) REVERT: B 121 GLU cc_start: 0.4749 (mm-30) cc_final: 0.4140 (mm-30) REVERT: B 126 PHE cc_start: 0.4907 (OUTLIER) cc_final: 0.4146 (t80) REVERT: B 186 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: B 226 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6534 (tmm160) REVERT: B 256 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7186 (ttm170) REVERT: B 753 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7329 (tmt170) outliers start: 25 outliers final: 12 residues processed: 155 average time/residue: 1.4288 time to fit residues: 238.3465 Evaluate side-chains 163 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 0.0970 chunk 90 optimal weight: 0.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12198 Z= 0.223 Angle : 0.598 10.952 16506 Z= 0.301 Chirality : 0.039 0.175 1802 Planarity : 0.005 0.076 2060 Dihedral : 4.116 26.721 1612 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.10 % Allowed : 14.39 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.22), residues: 1418 helix: 2.13 (0.16), residues: 890 sheet: -0.97 (0.74), residues: 48 loop : -1.84 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 PHE 0.014 0.001 PHE A 126 TYR 0.010 0.001 TYR A 687 ARG 0.011 0.000 ARG B 461 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 497 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7307 (mt) REVERT: A 500 MET cc_start: 0.6437 (mtt) cc_final: 0.6019 (mtt) REVERT: A 578 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6180 (tt0) REVERT: A 753 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.5740 (tmt90) REVERT: B 121 GLU cc_start: 0.4755 (mm-30) cc_final: 0.4133 (mm-30) REVERT: B 126 PHE cc_start: 0.4937 (OUTLIER) cc_final: 0.4167 (t80) REVERT: B 186 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: B 226 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6657 (tmm160) REVERT: B 256 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7202 (ttm170) REVERT: B 753 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7338 (tmt170) outliers start: 27 outliers final: 12 residues processed: 152 average time/residue: 1.4623 time to fit residues: 241.6377 Evaluate side-chains 160 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.0670 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102375 restraints weight = 17417.887| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.22 r_work: 0.3127 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12198 Z= 0.186 Angle : 0.593 11.545 16506 Z= 0.297 Chirality : 0.039 0.158 1802 Planarity : 0.005 0.109 2060 Dihedral : 4.057 22.267 1610 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.10 % Allowed : 14.39 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1418 helix: 2.16 (0.17), residues: 890 sheet: -0.97 (0.73), residues: 48 loop : -1.82 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 427 HIS 0.011 0.001 HIS A 898 PHE 0.019 0.001 PHE A 505 TYR 0.012 0.001 TYR B 277 ARG 0.010 0.000 ARG B 461 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4762.29 seconds wall clock time: 85 minutes 57.40 seconds (5157.40 seconds total)