Starting phenix.real_space_refine on Mon Mar 11 05:20:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/03_2024/8huj_35041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/03_2024/8huj_35041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/03_2024/8huj_35041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/03_2024/8huj_35041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/03_2024/8huj_35041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/03_2024/8huj_35041.pdb" } resolution = 3.76 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= 0.007 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 P 99 5.49 5 Mg 3 5.21 5 S 35 5.16 5 C 4108 2.51 5 N 1261 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B ASP 799": "OD1" <-> "OD2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B ASP 856": "OD1" <-> "OD2" Residue "B GLU 859": "OE1" <-> "OE2" Residue "B GLU 870": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B GLU 882": "OE1" <-> "OE2" Residue "B GLU 883": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B ARG 937": "NH1" <-> "NH2" Residue "B TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 968": "OE1" <-> "OE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7143 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 372} Chain: "B" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1951 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain: "C" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2125 Unusual residues: {' MG': 3} Classifications: {'RNA': 99, 'undetermined': 3, 'water': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 3, 'rna3p_pur': 44, 'rna3p_pyr': 41} Link IDs: {'rna2p': 14, 'rna3p': 84, None: 4} Not linked: pdbres=" C C 785 " pdbres=" MG C 801 " Not linked: pdbres=" MG C 801 " pdbres=" MG C 802 " Not linked: pdbres=" MG C 802 " pdbres=" MG C 803 " Not linked: pdbres=" MG C 803 " pdbres="HOH C 901 " Chain breaks: 2 Time building chain proxies: 4.39, per 1000 atoms: 0.61 Number of scatterers: 7143 At special positions: 0 Unit cell: (100.98, 94.095, 119.34, 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) S 35 16.00 P 99 15.00 Mg 3 11.99 O 1637 8.00 N 1261 7.00 C 4108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 865.1 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1186 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 65.1% alpha, 6.9% beta 37 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 4.101A pdb=" N ASN A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.564A pdb=" N GLY A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.207A pdb=" N PHE A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 139 through 150 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.585A pdb=" N LYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 257 through 269 removed outlier: 4.416A pdb=" N ASP A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.570A pdb=" N ASP A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.926A pdb=" N HIS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 removed outlier: 3.555A pdb=" N ARG A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.310A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 771 Processing helix chain 'B' and resid 775 through 785 removed outlier: 3.714A pdb=" N LEU B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 808 Processing helix chain 'B' and resid 811 through 822 removed outlier: 3.574A pdb=" N LEU B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 852 Processing helix chain 'B' and resid 853 through 871 removed outlier: 3.807A pdb=" N ASP B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU B 867 " --> pdb=" O LYS B 863 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 908 removed outlier: 3.609A pdb=" N LEU B 908 " --> pdb=" O GLU B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 926 removed outlier: 3.591A pdb=" N MET B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 921 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 922 " --> pdb=" O ASP B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 947 removed outlier: 5.967A pdb=" N LYS B 944 " --> pdb=" O THR B 940 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 945 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 951 through 969 removed outlier: 3.570A pdb=" N PHE B 959 " --> pdb=" O MET B 955 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN B 960 " --> pdb=" O ASP B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 988 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 removed outlier: 6.462A pdb=" N HIS A 132 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 104 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP A 182 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 106 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 179 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 212 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 181 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 72 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N SER A 213 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 74 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 removed outlier: 6.490A pdb=" N SER A 300 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 275 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 328 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 277 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 827 through 828 269 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1756 1.33 - 1.46: 1895 1.46 - 1.58: 3551 1.58 - 1.70: 195 1.70 - 1.82: 60 Bond restraints: 7457 Sorted by residual: bond pdb=" N VAL B 835 " pdb=" CA VAL B 835 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.32e-02 5.74e+03 8.07e+00 bond pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.87e+00 bond pdb=" N MET A 187 " pdb=" CA MET A 187 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N LYS A 369 " pdb=" CA LYS A 369 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.19e-02 7.06e+03 6.73e+00 bond pdb=" N VAL A 180 " pdb=" CA VAL A 180 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.41e+00 ... (remaining 7452 not shown) Histogram of bond angle deviations from ideal: 96.27 - 103.80: 334 103.80 - 111.34: 3470 111.34 - 118.87: 2956 118.87 - 126.40: 3437 126.40 - 133.94: 330 Bond angle restraints: 10527 Sorted by residual: angle pdb=" CA PHE B 839 " pdb=" CB PHE B 839 " pdb=" CG PHE B 839 " ideal model delta sigma weight residual 113.80 119.00 -5.20 1.00e+00 1.00e+00 2.70e+01 angle pdb=" O3' U C 778 " pdb=" C3' U C 778 " pdb=" C2' U C 778 " ideal model delta sigma weight residual 113.70 121.48 -7.78 1.50e+00 4.44e-01 2.69e+01 angle pdb=" N ARG A 368 " pdb=" CA ARG A 368 " pdb=" C ARG A 368 " ideal model delta sigma weight residual 111.28 106.15 5.13 1.09e+00 8.42e-01 2.22e+01 angle pdb=" C4' U C 778 " pdb=" C3' U C 778 " pdb=" O3' U C 778 " ideal model delta sigma weight residual 113.00 119.98 -6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" CA VAL B 835 " pdb=" C VAL B 835 " pdb=" O VAL B 835 " ideal model delta sigma weight residual 121.92 117.02 4.90 1.17e+00 7.31e-01 1.75e+01 ... (remaining 10522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 4196 31.18 - 62.37: 405 62.37 - 93.55: 108 93.55 - 124.74: 2 124.74 - 155.92: 1 Dihedral angle restraints: 4712 sinusoidal: 2893 harmonic: 1819 Sorted by residual: dihedral pdb=" C5' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" O3' A C 687 " ideal model delta sinusoidal sigma weight residual 147.00 108.10 38.90 1 8.00e+00 1.56e-02 3.33e+01 dihedral pdb=" O4' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" C2' A C 687 " ideal model delta sinusoidal sigma weight residual 24.00 -8.41 32.41 1 8.00e+00 1.56e-02 2.34e+01 dihedral pdb=" O4' A C 687 " pdb=" C1' A C 687 " pdb=" N9 A C 687 " pdb=" C4 A C 687 " ideal model delta sinusoidal sigma weight residual -106.00 -172.85 66.85 1 1.70e+01 3.46e-03 2.02e+01 ... (remaining 4709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1157 0.101 - 0.202: 94 0.202 - 0.302: 22 0.302 - 0.403: 1 0.403 - 0.504: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" C3' U C 778 " pdb=" C4' U C 778 " pdb=" O3' U C 778 " pdb=" C2' U C 778 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" C3' A C 771 " pdb=" C4' A C 771 " pdb=" O3' A C 771 " pdb=" C2' A C 771 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" P G C 766 " pdb=" OP1 G C 766 " pdb=" OP2 G C 766 " pdb=" O5' G C 766 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1272 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 158 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.48e+00 pdb=" C THR A 158 " 0.047 2.00e-02 2.50e+03 pdb=" O THR A 158 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 64 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 65 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 86 " 0.013 2.00e-02 2.50e+03 1.39e-02 3.37e+00 pdb=" CG PHE A 86 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 86 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 86 " 0.002 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 829 2.74 - 3.28: 7178 3.28 - 3.82: 13651 3.82 - 4.36: 15716 4.36 - 4.90: 22689 Nonbonded interactions: 60063 Sorted by model distance: nonbonded pdb=" O ASP A 348 " pdb=" NH1 ARG A 359 " model vdw 2.203 2.520 nonbonded pdb=" O CYS B 936 " pdb=" OG1 THR B 940 " model vdw 2.209 2.440 nonbonded pdb=" O ILE A 246 " pdb=" NE2 GLN A 248 " model vdw 2.244 2.520 nonbonded pdb=" O2 C C 746 " pdb=" N6 A C 750 " model vdw 2.249 2.520 nonbonded pdb=" N GLU A 379 " pdb=" OE1 GLU A 379 " model vdw 2.278 2.520 ... (remaining 60058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.940 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.570 Find NCS groups from input model: 0.150 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.005 0.038 7457 Z= 0.314 Angle : 0.828 9.832 10527 Z= 0.518 Chirality : 0.062 0.504 1275 Planarity : 0.004 0.048 979 Dihedral : 22.476 155.919 3526 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.51 % Allowed : 26.21 % Favored : 71.27 % 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: -0.39 (0.34), residues: 617 helix: 0.44 (0.28), residues: 340 sheet: -0.76 (0.64), residues: 61 loop : -1.08 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 287 HIS 0.003 0.001 HIS A 303 PHE 0.032 0.003 PHE A 86 TYR 0.009 0.002 TYR A 170 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.5083 (mtm) cc_final: 0.4264 (mtm) REVERT: A 228 MET cc_start: 0.4751 (tmm) cc_final: 0.4451 (tmm) REVERT: B 845 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7996 (t0) REVERT: B 890 ILE cc_start: 0.8839 (mm) cc_final: 0.8495 (mm) outliers start: 14 outliers final: 5 residues processed: 75 average time/residue: 0.2285 time to fit residues: 22.4737 Evaluate side-chains 66 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 845 ASN Chi-restraints excluded: chain B residue 893 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7457 Z= 0.192 Angle : 0.590 7.960 10527 Z= 0.301 Chirality : 0.037 0.175 1275 Planarity : 0.004 0.043 979 Dihedral : 21.708 160.791 2234 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.59 % Allowed : 25.67 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.35), residues: 617 helix: 0.85 (0.27), residues: 361 sheet: -0.79 (0.59), residues: 68 loop : -0.77 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 287 HIS 0.003 0.001 HIS B 927 PHE 0.028 0.002 PHE B 977 TYR 0.010 0.002 TYR A 48 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.2731 (ptt) cc_final: 0.1703 (mtm) REVERT: A 187 MET cc_start: 0.6377 (tmm) cc_final: 0.5892 (ppp) REVERT: A 228 MET cc_start: 0.4504 (tmm) cc_final: 0.4143 (tmm) REVERT: A 293 HIS cc_start: 0.7763 (t-90) cc_final: 0.7531 (t-90) REVERT: B 845 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8255 (t0) REVERT: B 853 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6917 (ptpt) REVERT: B 890 ILE cc_start: 0.8701 (mm) cc_final: 0.8394 (mm) outliers start: 20 outliers final: 12 residues processed: 84 average time/residue: 0.2015 time to fit residues: 22.5745 Evaluate side-chains 74 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 845 ASN Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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: 0.7775 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7457 Z= 0.281 Angle : 0.634 9.068 10527 Z= 0.321 Chirality : 0.038 0.197 1275 Planarity : 0.004 0.039 979 Dihedral : 21.744 158.961 2228 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.39 % Allowed : 24.96 % Favored : 69.66 % 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: 0.26 (0.35), residues: 617 helix: 0.89 (0.27), residues: 356 sheet: -0.71 (0.60), residues: 68 loop : -0.67 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 287 HIS 0.004 0.001 HIS A 303 PHE 0.044 0.003 PHE B 977 TYR 0.017 0.002 TYR A 48 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 69 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 181 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7354 (tp) REVERT: A 187 MET cc_start: 0.6606 (tmm) cc_final: 0.6044 (ppp) REVERT: A 193 LYS cc_start: 0.4906 (OUTLIER) cc_final: 0.4669 (tptt) REVERT: A 228 MET cc_start: 0.4781 (tmm) cc_final: 0.4350 (tmm) REVERT: A 293 HIS cc_start: 0.7751 (t-90) cc_final: 0.7531 (t-90) REVERT: B 853 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6751 (ptpt) REVERT: B 855 LYS cc_start: 0.7281 (mmtm) cc_final: 0.6866 (mttm) REVERT: B 986 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6955 (ttt-90) outliers start: 30 outliers final: 20 residues processed: 93 average time/residue: 0.2132 time to fit residues: 26.1615 Evaluate side-chains 89 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 65 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 40.0000 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7457 Z= 0.273 Angle : 0.614 8.754 10527 Z= 0.313 Chirality : 0.038 0.197 1275 Planarity : 0.004 0.040 979 Dihedral : 21.608 158.668 2225 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 7.18 % Allowed : 25.67 % Favored : 67.15 % 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: 0.25 (0.35), residues: 617 helix: 0.90 (0.27), residues: 356 sheet: -0.82 (0.61), residues: 68 loop : -0.66 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 27 HIS 0.003 0.001 HIS A 303 PHE 0.041 0.002 PHE B 977 TYR 0.015 0.002 TYR A 267 ARG 0.007 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 69 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 143 GLU cc_start: 0.2324 (OUTLIER) cc_final: 0.1917 (tp30) REVERT: A 181 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7464 (tp) REVERT: A 187 MET cc_start: 0.6753 (tmm) cc_final: 0.6257 (ppp) REVERT: A 228 MET cc_start: 0.4484 (tmm) cc_final: 0.3930 (tmm) REVERT: A 258 TRP cc_start: 0.8416 (m-10) cc_final: 0.8063 (m-10) REVERT: A 293 HIS cc_start: 0.7839 (t-90) cc_final: 0.7618 (t-90) REVERT: B 776 PHE cc_start: 0.8015 (t80) cc_final: 0.7541 (t80) REVERT: B 791 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: B 855 LYS cc_start: 0.7075 (mmtm) cc_final: 0.6673 (mttm) REVERT: B 986 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6997 (ttt-90) outliers start: 40 outliers final: 24 residues processed: 102 average time/residue: 0.1979 time to fit residues: 27.1036 Evaluate side-chains 96 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 68 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 50.0000 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7457 Z= 0.205 Angle : 0.564 8.600 10527 Z= 0.287 Chirality : 0.036 0.181 1275 Planarity : 0.003 0.041 979 Dihedral : 21.347 159.558 2221 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.46 % Allowed : 27.65 % Favored : 65.89 % 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: 0.44 (0.35), residues: 617 helix: 1.10 (0.27), residues: 360 sheet: -0.51 (0.66), residues: 62 loop : -0.86 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 287 HIS 0.003 0.001 HIS A 303 PHE 0.026 0.002 PHE B 977 TYR 0.011 0.002 TYR A 48 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 69 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 143 GLU cc_start: 0.2224 (OUTLIER) cc_final: 0.1986 (mt-10) REVERT: A 181 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7334 (tp) REVERT: A 187 MET cc_start: 0.6701 (tmm) cc_final: 0.6230 (ppp) REVERT: A 228 MET cc_start: 0.4358 (tmm) cc_final: 0.4061 (tmm) REVERT: A 258 TRP cc_start: 0.8338 (m-10) cc_final: 0.8032 (m-10) REVERT: A 277 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8639 (tp) REVERT: A 293 HIS cc_start: 0.7736 (t-90) cc_final: 0.7516 (t-90) REVERT: B 776 PHE cc_start: 0.7918 (t80) cc_final: 0.7668 (t80) REVERT: B 855 LYS cc_start: 0.7099 (mmtm) cc_final: 0.6752 (mttm) REVERT: B 977 PHE cc_start: 0.7891 (m-10) cc_final: 0.7672 (m-80) REVERT: B 986 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6995 (ttt-90) outliers start: 36 outliers final: 27 residues processed: 99 average time/residue: 0.1801 time to fit residues: 24.6653 Evaluate side-chains 97 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 66 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7457 Z= 0.307 Angle : 0.642 8.953 10527 Z= 0.327 Chirality : 0.039 0.205 1275 Planarity : 0.004 0.039 979 Dihedral : 21.566 158.594 2221 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.90 % Allowed : 26.21 % Favored : 65.89 % 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: 0.29 (0.35), residues: 617 helix: 0.90 (0.27), residues: 360 sheet: -0.44 (0.67), residues: 62 loop : -0.80 (0.50), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 287 HIS 0.003 0.001 HIS A 303 PHE 0.026 0.003 PHE B 977 TYR 0.018 0.002 TYR A 48 ARG 0.004 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 64 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.5366 (mtm) cc_final: 0.5056 (mtm) REVERT: A 181 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 187 MET cc_start: 0.6772 (tmm) cc_final: 0.6362 (ppp) REVERT: A 228 MET cc_start: 0.4421 (tmm) cc_final: 0.4010 (tmm) REVERT: A 293 HIS cc_start: 0.7830 (t-90) cc_final: 0.7624 (t-90) REVERT: B 776 PHE cc_start: 0.7997 (t80) cc_final: 0.7721 (t80) REVERT: B 791 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: B 804 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.7998 (ttmm) REVERT: B 855 LYS cc_start: 0.7125 (mmtm) cc_final: 0.6782 (mttm) REVERT: B 977 PHE cc_start: 0.7979 (m-10) cc_final: 0.7718 (m-10) REVERT: B 986 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7023 (ttt-90) outliers start: 44 outliers final: 33 residues processed: 101 average time/residue: 0.1804 time to fit residues: 25.0349 Evaluate side-chains 100 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 63 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 804 LYS Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7457 Z= 0.214 Angle : 0.574 8.860 10527 Z= 0.293 Chirality : 0.037 0.185 1275 Planarity : 0.003 0.041 979 Dihedral : 21.391 159.058 2221 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 7.72 % Allowed : 27.29 % Favored : 64.99 % 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: 0.54 (0.35), residues: 617 helix: 1.15 (0.27), residues: 359 sheet: -0.41 (0.67), residues: 62 loop : -0.75 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 287 HIS 0.003 0.001 HIS A 303 PHE 0.019 0.002 PHE B 977 TYR 0.012 0.002 TYR A 48 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 64 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.2178 (OUTLIER) cc_final: 0.1906 (mt-10) REVERT: A 178 MET cc_start: 0.5192 (mtm) cc_final: 0.4948 (mtm) REVERT: A 181 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7418 (tp) REVERT: A 228 MET cc_start: 0.4228 (tmm) cc_final: 0.3955 (tmm) REVERT: A 258 TRP cc_start: 0.8189 (m-10) cc_final: 0.7988 (m-10) REVERT: A 293 HIS cc_start: 0.7734 (t-90) cc_final: 0.7519 (t-90) REVERT: B 776 PHE cc_start: 0.8017 (t80) cc_final: 0.7732 (t80) REVERT: B 791 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: B 855 LYS cc_start: 0.7101 (mmtm) cc_final: 0.6763 (mttm) REVERT: B 977 PHE cc_start: 0.7906 (m-10) cc_final: 0.7653 (m-10) REVERT: B 986 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7008 (ttt-90) outliers start: 43 outliers final: 32 residues processed: 100 average time/residue: 0.1682 time to fit residues: 23.3842 Evaluate side-chains 100 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 64 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7457 Z= 0.198 Angle : 0.560 9.053 10527 Z= 0.284 Chirality : 0.036 0.181 1275 Planarity : 0.003 0.041 979 Dihedral : 21.259 159.091 2221 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 7.36 % Allowed : 27.29 % Favored : 65.35 % 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: 0.67 (0.35), residues: 617 helix: 1.30 (0.28), residues: 359 sheet: -0.35 (0.67), residues: 62 loop : -0.80 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 287 HIS 0.002 0.001 HIS A 303 PHE 0.018 0.002 PHE B 977 TYR 0.011 0.001 TYR A 48 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 66 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 127 MET cc_start: 0.6963 (mmm) cc_final: 0.6722 (mmm) REVERT: A 143 GLU cc_start: 0.2239 (OUTLIER) cc_final: 0.1989 (mt-10) REVERT: A 181 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7395 (tp) REVERT: A 228 MET cc_start: 0.4287 (tmm) cc_final: 0.3978 (tmm) REVERT: A 258 TRP cc_start: 0.8223 (m-10) cc_final: 0.7953 (m-10) REVERT: A 293 HIS cc_start: 0.7709 (t-90) cc_final: 0.7491 (t-90) REVERT: B 776 PHE cc_start: 0.7887 (t80) cc_final: 0.7411 (t80) REVERT: B 791 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: B 855 LYS cc_start: 0.7042 (mmtm) cc_final: 0.6700 (mttm) REVERT: B 890 ILE cc_start: 0.8869 (mm) cc_final: 0.8597 (mm) REVERT: B 977 PHE cc_start: 0.8015 (m-10) cc_final: 0.7759 (m-10) REVERT: B 986 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7067 (ttt-90) outliers start: 41 outliers final: 35 residues processed: 99 average time/residue: 0.1741 time to fit residues: 23.7553 Evaluate side-chains 103 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 64 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 67 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7457 Z= 0.220 Angle : 0.576 9.259 10527 Z= 0.292 Chirality : 0.037 0.186 1275 Planarity : 0.003 0.041 979 Dihedral : 21.312 158.850 2221 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 7.90 % Allowed : 27.29 % Favored : 64.81 % 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: 0.64 (0.35), residues: 617 helix: 1.24 (0.27), residues: 359 sheet: -0.26 (0.68), residues: 62 loop : -0.78 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 287 HIS 0.003 0.001 HIS A 303 PHE 0.035 0.002 PHE A 86 TYR 0.013 0.002 TYR A 48 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 66 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 127 MET cc_start: 0.7036 (mmm) cc_final: 0.6771 (mmm) REVERT: A 143 GLU cc_start: 0.2168 (OUTLIER) cc_final: 0.1894 (mt-10) REVERT: A 178 MET cc_start: 0.5780 (mtm) cc_final: 0.5475 (mtm) REVERT: A 181 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7387 (tp) REVERT: A 187 MET cc_start: 0.5657 (ppp) cc_final: 0.5163 (ppp) REVERT: A 228 MET cc_start: 0.4285 (tmm) cc_final: 0.3952 (tmm) REVERT: A 258 TRP cc_start: 0.8247 (m-10) cc_final: 0.7996 (m-10) REVERT: A 293 HIS cc_start: 0.7716 (t-90) cc_final: 0.7493 (t-90) REVERT: B 776 PHE cc_start: 0.7941 (t80) cc_final: 0.7424 (t80) REVERT: B 791 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: B 804 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.7961 (ttmm) REVERT: B 855 LYS cc_start: 0.7087 (mmtm) cc_final: 0.6747 (mttm) REVERT: B 977 PHE cc_start: 0.7984 (m-10) cc_final: 0.7722 (m-10) REVERT: B 986 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7033 (ttt-90) outliers start: 44 outliers final: 37 residues processed: 102 average time/residue: 0.1830 time to fit residues: 25.8913 Evaluate side-chains 106 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 64 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 804 LYS Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7457 Z= 0.263 Angle : 0.609 9.554 10527 Z= 0.308 Chirality : 0.038 0.196 1275 Planarity : 0.003 0.040 979 Dihedral : 21.419 158.567 2221 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 7.72 % Allowed : 27.65 % Favored : 64.63 % 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: 0.50 (0.35), residues: 617 helix: 1.09 (0.27), residues: 359 sheet: -0.28 (0.67), residues: 62 loop : -0.77 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 287 HIS 0.003 0.001 HIS A 153 PHE 0.036 0.003 PHE A 86 TYR 0.016 0.002 TYR A 48 ARG 0.004 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 67 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 127 MET cc_start: 0.7046 (mmm) cc_final: 0.6788 (mmm) REVERT: A 143 GLU cc_start: 0.2400 (OUTLIER) cc_final: 0.2133 (mt-10) REVERT: A 181 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7461 (tp) REVERT: A 187 MET cc_start: 0.5702 (ppp) cc_final: 0.5198 (ppp) REVERT: A 258 TRP cc_start: 0.8254 (m-10) cc_final: 0.7992 (m-10) REVERT: A 293 HIS cc_start: 0.7726 (t-90) cc_final: 0.7508 (t-90) REVERT: B 776 PHE cc_start: 0.8020 (t80) cc_final: 0.7541 (t80) REVERT: B 791 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: B 804 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.7991 (ttmm) REVERT: B 855 LYS cc_start: 0.7033 (mmtm) cc_final: 0.6692 (mttm) REVERT: B 977 PHE cc_start: 0.7998 (m-10) cc_final: 0.7733 (m-10) REVERT: B 986 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6978 (ttt-90) outliers start: 43 outliers final: 36 residues processed: 102 average time/residue: 0.1828 time to fit residues: 25.2743 Evaluate side-chains 108 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 67 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 804 LYS Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 6.9990 chunk 7 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 3 optimal weight: 0.0470 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.071215 restraints weight = 22072.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073394 restraints weight = 10688.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074709 restraints weight = 7385.090| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7457 Z= 0.208 Angle : 0.567 9.395 10527 Z= 0.288 Chirality : 0.037 0.183 1275 Planarity : 0.003 0.041 979 Dihedral : 21.260 158.917 2221 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 7.54 % Allowed : 28.37 % Favored : 64.09 % 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: 0.63 (0.35), residues: 617 helix: 1.28 (0.27), residues: 359 sheet: -0.27 (0.73), residues: 55 loop : -0.88 (0.47), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 287 HIS 0.002 0.001 HIS A 303 PHE 0.035 0.003 PHE A 86 TYR 0.012 0.002 TYR A 48 ARG 0.003 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1308.20 seconds wall clock time: 24 minutes 52.49 seconds (1492.49 seconds total)