Starting phenix.real_space_refine on Tue Sep 24 14:58:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/09_2024/6vxo_21446.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/09_2024/6vxo_21446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/09_2024/6vxo_21446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/09_2024/6vxo_21446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/09_2024/6vxo_21446.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxo_21446/09_2024/6vxo_21446.cif" } resolution = 3.5 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 24 5.16 5 C 5548 2.51 5 N 1184 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "C" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 208 Unusual residues: {'POV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: E Time building chain proxies: 5.61, per 1000 atoms: 0.70 Number of scatterers: 8048 At special positions: 0 Unit cell: (123.654, 123.654, 65.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 12 15.00 O 1280 8.00 N 1184 7.00 C 5548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 957.0 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 74.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 23 through 43 removed outlier: 4.283A pdb=" N PHE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 52 through 77 removed outlier: 3.922A pdb=" N PHE A 56 " --> pdb=" O HIS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.545A pdb=" N TRP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.893A pdb=" N LEU A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 122' Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 148 through 169 removed outlier: 3.665A pdb=" N MET A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.744A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 235 removed outlier: 3.959A pdb=" N PHE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 43 removed outlier: 4.284A pdb=" N PHE C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 52 through 77 removed outlier: 3.923A pdb=" N PHE C 56 " --> pdb=" O HIS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 106 removed outlier: 3.545A pdb=" N TRP C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.893A pdb=" N LEU C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 122' Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 148 through 169 removed outlier: 3.664A pdb=" N MET C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 187 through 192 removed outlier: 3.745A pdb=" N VAL C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 235 removed outlier: 3.960A pdb=" N PHE C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 43 removed outlier: 4.284A pdb=" N PHE D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 52 through 77 removed outlier: 3.922A pdb=" N PHE D 56 " --> pdb=" O HIS D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 106 removed outlier: 3.545A pdb=" N TRP D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 removed outlier: 3.893A pdb=" N LEU D 121 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 117 through 122' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 130 through 143 Processing helix chain 'D' and resid 148 through 169 removed outlier: 3.664A pdb=" N MET D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.745A pdb=" N VAL D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 235 removed outlier: 3.959A pdb=" N PHE D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 43 removed outlier: 4.285A pdb=" N PHE E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 52 through 77 removed outlier: 3.923A pdb=" N PHE E 56 " --> pdb=" O HIS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 106 removed outlier: 3.546A pdb=" N TRP E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.892A pdb=" N LEU E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 122' Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'E' and resid 130 through 143 Processing helix chain 'E' and resid 148 through 169 removed outlier: 3.665A pdb=" N MET E 167 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.744A pdb=" N VAL E 191 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 206 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 211 through 235 removed outlier: 3.959A pdb=" N PHE E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 220 " --> pdb=" O VAL E 216 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1284 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: 1.76 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1084 1.30 - 1.43: 2299 1.43 - 1.55: 4723 1.55 - 1.68: 90 1.68 - 1.80: 48 Bond restraints: 8244 Sorted by residual: bond pdb=" C31 POV D 302 " pdb=" O31 POV D 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C31 POV C 302 " pdb=" O31 POV C 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C31 POV E 302 " pdb=" O31 POV E 302 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C31 POV A 303 " pdb=" O31 POV A 303 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C31 POV C 301 " pdb=" O31 POV C 301 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.28e+01 ... (remaining 8239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 10386 2.32 - 4.65: 483 4.65 - 6.97: 163 6.97 - 9.30: 48 9.30 - 11.62: 32 Bond angle restraints: 11112 Sorted by residual: angle pdb=" N VAL A 114 " pdb=" CA VAL A 114 " pdb=" C VAL A 114 " ideal model delta sigma weight residual 111.91 107.01 4.90 8.90e-01 1.26e+00 3.03e+01 angle pdb=" N VAL C 114 " pdb=" CA VAL C 114 " pdb=" C VAL C 114 " ideal model delta sigma weight residual 111.91 107.03 4.88 8.90e-01 1.26e+00 3.01e+01 angle pdb=" N VAL E 114 " pdb=" CA VAL E 114 " pdb=" C VAL E 114 " ideal model delta sigma weight residual 111.91 107.03 4.88 8.90e-01 1.26e+00 3.01e+01 angle pdb=" N VAL D 114 " pdb=" CA VAL D 114 " pdb=" C VAL D 114 " ideal model delta sigma weight residual 111.91 107.04 4.87 8.90e-01 1.26e+00 3.00e+01 angle pdb=" O13 POV A 303 " pdb=" P POV A 303 " pdb=" O14 POV A 303 " ideal model delta sigma weight residual 121.11 109.49 11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 11107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 4071 24.08 - 48.16: 594 48.16 - 72.24: 175 72.24 - 96.32: 48 96.32 - 120.40: 12 Dihedral angle restraints: 4900 sinusoidal: 2232 harmonic: 2668 Sorted by residual: dihedral pdb=" CA VAL C 109 " pdb=" C VAL C 109 " pdb=" N GLU C 110 " pdb=" CA GLU C 110 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL E 235 " pdb=" C VAL E 235 " pdb=" N ASN E 236 " pdb=" CA ASN E 236 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL D 235 " pdb=" C VAL D 235 " pdb=" N ASN D 236 " pdb=" CA ASN D 236 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 587 0.027 - 0.053: 338 0.053 - 0.079: 207 0.079 - 0.106: 93 0.106 - 0.132: 35 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA VAL A 235 " pdb=" N VAL A 235 " pdb=" C VAL A 235 " pdb=" CB VAL A 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL D 235 " pdb=" N VAL D 235 " pdb=" C VAL D 235 " pdb=" CB VAL D 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL C 235 " pdb=" N VAL C 235 " pdb=" C VAL C 235 " pdb=" CB VAL C 235 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1257 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 234 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE D 234 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE D 234 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL D 235 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 234 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE C 234 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 234 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 235 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 234 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ILE A 234 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 234 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 235 " -0.010 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 307 2.68 - 3.24: 8646 3.24 - 3.79: 12731 3.79 - 4.35: 15410 4.35 - 4.90: 25309 Nonbonded interactions: 62403 Sorted by model distance: nonbonded pdb=" O TYR D 214 " pdb=" OG SER D 217 " model vdw 2.125 3.040 nonbonded pdb=" O TYR A 214 " pdb=" OG SER A 217 " model vdw 2.125 3.040 nonbonded pdb=" O TYR E 214 " pdb=" OG SER E 217 " model vdw 2.126 3.040 nonbonded pdb=" O TYR C 214 " pdb=" OG SER C 217 " model vdw 2.126 3.040 nonbonded pdb=" O PHE E 161 " pdb=" OH TYR E 214 " model vdw 2.219 3.040 ... (remaining 62398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 240 or resid 301 through 302)) selection = chain 'C' selection = (chain 'D' and (resid 15 through 240 or resid 301 through 302)) selection = (chain 'E' and (resid 15 through 240 or resid 301 through 302)) } 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: 0.820 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.360 Find NCS groups from input model: 0.340 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.097 8244 Z= 0.771 Angle : 1.401 11.619 11112 Z= 0.585 Chirality : 0.047 0.132 1260 Planarity : 0.005 0.035 1272 Dihedral : 24.970 120.396 3156 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.17 % Favored : 87.39 % Rotamer: Outliers : 21.57 % Allowed : 21.08 % Favored : 57.35 % 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: -3.90 (0.24), residues: 896 helix: -1.88 (0.17), residues: 640 sheet: None (None), residues: 0 loop : -4.16 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.003 0.001 HIS C 171 PHE 0.017 0.002 PHE C 205 TYR 0.007 0.001 TYR A 159 ARG 0.002 0.000 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 207 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8605 (m-80) cc_final: 0.8347 (m-80) REVERT: A 47 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: A 54 TRP cc_start: 0.7193 (p-90) cc_final: 0.6970 (p-90) REVERT: A 63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9139 (mm) REVERT: A 65 TRP cc_start: 0.8015 (m100) cc_final: 0.7668 (t-100) REVERT: A 70 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8263 (tp30) REVERT: A 103 GLU cc_start: 0.8881 (tp30) cc_final: 0.8587 (tp30) REVERT: A 230 PHE cc_start: 0.7810 (t80) cc_final: 0.7604 (t80) REVERT: C 45 TYR cc_start: 0.8575 (m-80) cc_final: 0.8319 (m-80) REVERT: C 47 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7791 (ttm-80) REVERT: C 54 TRP cc_start: 0.7194 (p-90) cc_final: 0.6965 (p-90) REVERT: C 63 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9140 (mm) REVERT: C 65 TRP cc_start: 0.8002 (m100) cc_final: 0.7624 (t-100) REVERT: C 70 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8243 (tp30) REVERT: C 103 GLU cc_start: 0.8868 (tp30) cc_final: 0.8620 (tp30) REVERT: C 115 LEU cc_start: 0.8801 (mt) cc_final: 0.8526 (mt) REVERT: C 230 PHE cc_start: 0.7810 (t80) cc_final: 0.7598 (t80) REVERT: D 45 TYR cc_start: 0.8603 (m-80) cc_final: 0.8339 (m-80) REVERT: D 47 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7809 (ttm-80) REVERT: D 54 TRP cc_start: 0.7218 (p-90) cc_final: 0.6990 (p-90) REVERT: D 63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9132 (mm) REVERT: D 65 TRP cc_start: 0.7986 (m100) cc_final: 0.7618 (t-100) REVERT: D 70 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8265 (tp30) REVERT: D 103 GLU cc_start: 0.8885 (tp30) cc_final: 0.8677 (tp30) REVERT: D 115 LEU cc_start: 0.8844 (mt) cc_final: 0.8593 (mt) REVERT: D 230 PHE cc_start: 0.7821 (t80) cc_final: 0.7598 (t80) REVERT: E 45 TYR cc_start: 0.8632 (m-80) cc_final: 0.8402 (m-80) REVERT: E 47 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7820 (ttm-80) REVERT: E 54 TRP cc_start: 0.7227 (p-90) cc_final: 0.7024 (p-90) REVERT: E 63 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9115 (mm) REVERT: E 65 TRP cc_start: 0.8109 (m100) cc_final: 0.7658 (t-100) REVERT: E 70 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8274 (tp30) REVERT: E 115 LEU cc_start: 0.8688 (mt) cc_final: 0.8449 (mt) REVERT: E 230 PHE cc_start: 0.7851 (t80) cc_final: 0.7623 (t80) outliers start: 176 outliers final: 141 residues processed: 336 average time/residue: 0.1454 time to fit residues: 70.4084 Evaluate side-chains 329 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 180 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 ASN Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 170 GLN A 181 GLN A 189 GLN A 237 ASN C 90 ASN C 170 GLN C 181 GLN C 189 GLN C 237 ASN D 90 ASN D 170 GLN D 181 GLN D 237 ASN E 90 ASN E 170 GLN E 181 GLN E 237 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8244 Z= 0.198 Angle : 0.622 6.048 11112 Z= 0.319 Chirality : 0.041 0.155 1260 Planarity : 0.003 0.020 1272 Dihedral : 23.708 109.764 1756 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 9.68 % Allowed : 23.53 % Favored : 66.79 % 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: -1.06 (0.29), residues: 896 helix: 0.27 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.92 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.001 0.001 HIS C 52 PHE 0.014 0.001 PHE D 205 TYR 0.012 0.002 TYR D 214 ARG 0.001 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 220 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8411 (m-80) cc_final: 0.8081 (m-80) REVERT: A 65 TRP cc_start: 0.7974 (m100) cc_final: 0.7634 (t-100) REVERT: A 207 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7426 (mm-30) REVERT: C 45 TYR cc_start: 0.8421 (m-80) cc_final: 0.8084 (m-80) REVERT: C 65 TRP cc_start: 0.7941 (m100) cc_final: 0.7611 (t-100) REVERT: C 207 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 231 ILE cc_start: 0.8670 (mt) cc_final: 0.8467 (mt) REVERT: D 45 TYR cc_start: 0.8421 (m-80) cc_final: 0.8069 (m-80) REVERT: D 53 LYS cc_start: 0.8343 (ttpt) cc_final: 0.8133 (tptp) REVERT: D 65 TRP cc_start: 0.7936 (m100) cc_final: 0.7591 (t-100) REVERT: D 138 ASP cc_start: 0.8235 (t0) cc_final: 0.8000 (t0) REVERT: D 207 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7362 (mm-30) REVERT: E 45 TYR cc_start: 0.8462 (m-80) cc_final: 0.8151 (m-80) REVERT: E 65 TRP cc_start: 0.8014 (m100) cc_final: 0.7662 (t-100) REVERT: E 202 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8805 (tpp-160) REVERT: E 207 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7366 (mm-30) outliers start: 79 outliers final: 38 residues processed: 287 average time/residue: 0.1409 time to fit residues: 59.2352 Evaluate side-chains 252 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN D 228 ASN E 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8244 Z= 0.193 Angle : 0.625 7.630 11112 Z= 0.316 Chirality : 0.043 0.161 1260 Planarity : 0.003 0.018 1272 Dihedral : 21.995 110.102 1546 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 10.54 % Allowed : 25.86 % Favored : 63.60 % 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: -0.21 (0.30), residues: 896 helix: 0.73 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -2.13 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 65 HIS 0.001 0.001 HIS E 22 PHE 0.025 0.001 PHE C 94 TYR 0.004 0.001 TYR E 214 ARG 0.001 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 229 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8240 (m-80) cc_final: 0.7866 (m-80) REVERT: A 63 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9206 (mm) REVERT: A 73 MET cc_start: 0.6426 (tpt) cc_final: 0.6222 (tpt) REVERT: A 158 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.9174 (m-80) REVERT: A 202 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8835 (tpp-160) REVERT: A 207 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7380 (mm-30) REVERT: C 45 TYR cc_start: 0.8291 (m-80) cc_final: 0.7911 (m-80) REVERT: C 73 MET cc_start: 0.6624 (tpt) cc_final: 0.6379 (tpt) REVERT: C 158 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.9166 (m-80) REVERT: C 207 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 45 TYR cc_start: 0.8242 (m-80) cc_final: 0.7872 (m-80) REVERT: D 63 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9193 (mm) REVERT: D 65 TRP cc_start: 0.7967 (m100) cc_final: 0.7683 (t-100) REVERT: D 158 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.9141 (m-80) REVERT: D 202 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8915 (tpp-160) REVERT: D 207 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7340 (mm-30) REVERT: E 45 TYR cc_start: 0.8323 (m-80) cc_final: 0.7953 (m-80) REVERT: E 63 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9198 (mm) REVERT: E 65 TRP cc_start: 0.7932 (m100) cc_final: 0.7704 (t-100) REVERT: E 158 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9130 (m-80) REVERT: E 207 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7348 (mm-30) outliers start: 86 outliers final: 47 residues processed: 299 average time/residue: 0.1378 time to fit residues: 60.4332 Evaluate side-chains 255 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 199 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8244 Z= 0.156 Angle : 0.640 12.137 11112 Z= 0.314 Chirality : 0.043 0.163 1260 Planarity : 0.003 0.024 1272 Dihedral : 20.641 103.113 1540 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 9.80 % Allowed : 26.23 % Favored : 63.97 % 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: -0.06 (0.30), residues: 896 helix: 0.70 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.93 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 54 HIS 0.003 0.001 HIS D 52 PHE 0.030 0.001 PHE D 94 TYR 0.009 0.001 TYR A 214 ARG 0.001 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 222 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8242 (m-80) cc_final: 0.7777 (m-80) REVERT: A 158 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.9050 (m-80) REVERT: C 45 TYR cc_start: 0.8239 (m-80) cc_final: 0.7785 (m-80) REVERT: C 63 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9102 (mm) REVERT: C 73 MET cc_start: 0.6156 (tpt) cc_final: 0.5904 (tpt) REVERT: C 138 ASP cc_start: 0.8190 (t0) cc_final: 0.7976 (t0) REVERT: C 158 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9083 (m-80) REVERT: C 230 PHE cc_start: 0.7666 (t80) cc_final: 0.7460 (t80) REVERT: D 63 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9103 (mm) REVERT: D 65 TRP cc_start: 0.7943 (m100) cc_final: 0.7567 (t-100) REVERT: D 158 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.9052 (m-80) REVERT: E 45 TYR cc_start: 0.8231 (m-80) cc_final: 0.7782 (m-80) REVERT: E 65 TRP cc_start: 0.7922 (m100) cc_final: 0.7593 (t-100) REVERT: E 158 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8989 (m-80) outliers start: 80 outliers final: 55 residues processed: 284 average time/residue: 0.1465 time to fit residues: 60.1034 Evaluate side-chains 264 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 203 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 72 optimal weight: 0.0770 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8244 Z= 0.180 Angle : 0.667 12.489 11112 Z= 0.322 Chirality : 0.042 0.163 1260 Planarity : 0.003 0.028 1272 Dihedral : 19.701 102.467 1530 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 9.56 % Allowed : 27.45 % Favored : 62.99 % 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: 0.08 (0.29), residues: 896 helix: 0.73 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.67 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.001 0.000 HIS C 52 PHE 0.024 0.001 PHE D 94 TYR 0.010 0.001 TYR A 214 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 224 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.8897 (p) REVERT: A 43 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7638 (pp20) REVERT: A 45 TYR cc_start: 0.8211 (m-80) cc_final: 0.7663 (m-80) REVERT: A 63 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9117 (mm) REVERT: A 158 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.9156 (m-80) REVERT: C 63 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9188 (mm) REVERT: C 158 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.9163 (m-80) REVERT: D 158 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9212 (m-80) REVERT: D 202 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8847 (tpp-160) REVERT: E 40 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.8937 (p) REVERT: E 43 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: E 45 TYR cc_start: 0.8207 (m-80) cc_final: 0.7672 (m-80) REVERT: E 158 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9121 (m-80) outliers start: 78 outliers final: 59 residues processed: 280 average time/residue: 0.1383 time to fit residues: 57.0125 Evaluate side-chains 280 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 210 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 228 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8244 Z= 0.225 Angle : 0.722 13.289 11112 Z= 0.344 Chirality : 0.044 0.169 1260 Planarity : 0.003 0.039 1272 Dihedral : 19.265 107.236 1528 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 10.66 % Allowed : 28.31 % Favored : 61.03 % 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: 0.18 (0.29), residues: 896 helix: 0.88 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.56 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 196 HIS 0.001 0.001 HIS E 171 PHE 0.021 0.001 PHE D 94 TYR 0.013 0.001 TYR D 214 ARG 0.002 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 215 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7602 (pp20) REVERT: A 45 TYR cc_start: 0.8207 (m-80) cc_final: 0.7657 (m-80) REVERT: A 63 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9074 (mm) REVERT: A 158 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.9124 (m-80) REVERT: A 220 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8653 (mt) REVERT: A 230 PHE cc_start: 0.7659 (t80) cc_final: 0.7408 (t80) REVERT: C 40 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.8851 (p) REVERT: C 43 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7509 (pp20) REVERT: C 45 TYR cc_start: 0.8257 (m-80) cc_final: 0.7742 (m-80) REVERT: C 63 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8972 (mt) REVERT: C 73 MET cc_start: 0.6327 (tpt) cc_final: 0.6102 (tpt) REVERT: C 158 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9138 (m-80) REVERT: C 220 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8818 (mm) REVERT: D 45 TYR cc_start: 0.8300 (m-80) cc_final: 0.7933 (m-80) REVERT: D 63 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9160 (mm) REVERT: D 158 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.9138 (m-80) REVERT: D 220 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8803 (mm) REVERT: E 40 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.8978 (p) REVERT: E 43 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7596 (pp20) REVERT: E 45 TYR cc_start: 0.8205 (m-80) cc_final: 0.7672 (m-80) REVERT: E 63 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9114 (mm) REVERT: E 158 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9119 (m-80) REVERT: E 220 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8792 (mm) outliers start: 87 outliers final: 59 residues processed: 279 average time/residue: 0.1407 time to fit residues: 57.9724 Evaluate side-chains 282 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 206 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 PHE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8244 Z= 0.201 Angle : 0.737 13.144 11112 Z= 0.346 Chirality : 0.043 0.176 1260 Planarity : 0.003 0.031 1272 Dihedral : 18.475 107.960 1526 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 9.56 % Allowed : 30.64 % Favored : 59.80 % 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: -0.09 (0.28), residues: 896 helix: 0.72 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -2.39 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 196 HIS 0.002 0.001 HIS C 52 PHE 0.020 0.001 PHE D 94 TYR 0.009 0.001 TYR C 214 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 213 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8230 (m-80) cc_final: 0.7731 (m-80) REVERT: A 63 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8992 (mm) REVERT: A 158 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9096 (m-80) REVERT: A 220 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8656 (mt) REVERT: C 40 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.8826 (p) REVERT: C 43 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7439 (pp20) REVERT: C 45 TYR cc_start: 0.8179 (m-80) cc_final: 0.7694 (m-80) REVERT: C 63 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8933 (mt) REVERT: C 73 MET cc_start: 0.6310 (tpt) cc_final: 0.6086 (tpt) REVERT: C 158 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9110 (m-80) REVERT: C 230 PHE cc_start: 0.7579 (t80) cc_final: 0.7356 (t80) REVERT: D 45 TYR cc_start: 0.8310 (m-80) cc_final: 0.7971 (m-80) REVERT: D 63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9037 (mm) REVERT: D 158 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.9084 (m-80) REVERT: E 40 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.8936 (p) REVERT: E 43 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7706 (pp20) REVERT: E 45 TYR cc_start: 0.8141 (m-80) cc_final: 0.7563 (m-80) REVERT: E 63 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9123 (mm) REVERT: E 158 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.9081 (m-80) outliers start: 78 outliers final: 62 residues processed: 269 average time/residue: 0.1451 time to fit residues: 57.5390 Evaluate side-chains 277 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 202 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 PHE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8244 Z= 0.200 Angle : 0.722 12.562 11112 Z= 0.343 Chirality : 0.044 0.175 1260 Planarity : 0.003 0.027 1272 Dihedral : 18.062 109.231 1526 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 10.17 % Allowed : 30.15 % Favored : 59.68 % 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: -0.03 (0.28), residues: 896 helix: 0.77 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -2.39 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 54 HIS 0.001 0.001 HIS A 22 PHE 0.019 0.001 PHE E 94 TYR 0.009 0.001 TYR A 214 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 204 time to evaluate : 0.865 Fit side-chains REVERT: A 45 TYR cc_start: 0.8168 (m-80) cc_final: 0.7713 (m-80) REVERT: A 63 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8937 (mm) REVERT: A 158 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.9088 (m-80) REVERT: A 220 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8553 (mt) REVERT: C 40 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.8882 (p) REVERT: C 43 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7432 (pp20) REVERT: C 45 TYR cc_start: 0.8197 (m-80) cc_final: 0.7726 (m-80) REVERT: C 63 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8900 (mt) REVERT: C 73 MET cc_start: 0.6367 (tpt) cc_final: 0.6146 (tpt) REVERT: C 158 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.9115 (m-80) REVERT: C 220 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8618 (mt) REVERT: D 45 TYR cc_start: 0.8256 (m-80) cc_final: 0.7929 (m-80) REVERT: D 63 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9017 (mm) REVERT: D 158 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.9099 (m-80) REVERT: D 220 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8618 (mt) REVERT: E 40 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.8993 (p) REVERT: E 43 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7758 (pp20) REVERT: E 63 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9131 (mm) REVERT: E 158 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.9085 (m-80) REVERT: E 220 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8705 (mt) outliers start: 83 outliers final: 62 residues processed: 259 average time/residue: 0.1516 time to fit residues: 56.9704 Evaluate side-chains 277 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 199 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 PHE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8244 Z= 0.228 Angle : 0.735 12.623 11112 Z= 0.354 Chirality : 0.044 0.181 1260 Planarity : 0.003 0.026 1272 Dihedral : 17.929 111.834 1524 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 10.17 % Allowed : 30.27 % Favored : 59.56 % 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: -0.03 (0.28), residues: 896 helix: 0.76 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.36 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 54 HIS 0.001 0.001 HIS D 171 PHE 0.018 0.001 PHE D 94 TYR 0.012 0.002 TYR E 214 ARG 0.002 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 197 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8220 (m-80) cc_final: 0.7792 (m-80) REVERT: A 63 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8920 (mm) REVERT: A 158 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: A 220 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8590 (mt) REVERT: C 40 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.8933 (p) REVERT: C 43 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7360 (pp20) REVERT: C 45 TYR cc_start: 0.8199 (m-80) cc_final: 0.7736 (m-80) REVERT: C 73 MET cc_start: 0.6446 (tpt) cc_final: 0.6224 (tpt) REVERT: C 158 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.9109 (m-80) REVERT: D 45 TYR cc_start: 0.8306 (m-80) cc_final: 0.7976 (m-80) REVERT: D 63 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8986 (mm) REVERT: D 158 PHE cc_start: 0.9375 (OUTLIER) cc_final: 0.9067 (m-80) REVERT: E 40 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9007 (p) REVERT: E 43 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7798 (pp20) REVERT: E 63 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9090 (mm) REVERT: E 158 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.9082 (m-80) REVERT: E 220 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8741 (mt) outliers start: 83 outliers final: 63 residues processed: 256 average time/residue: 0.1423 time to fit residues: 52.8713 Evaluate side-chains 273 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 197 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 PHE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 74 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8244 Z= 0.189 Angle : 0.723 12.398 11112 Z= 0.345 Chirality : 0.043 0.180 1260 Planarity : 0.003 0.025 1272 Dihedral : 17.201 108.274 1518 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 9.44 % Allowed : 31.25 % Favored : 59.31 % 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: -0.10 (0.28), residues: 896 helix: 0.75 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.48 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 54 HIS 0.001 0.000 HIS D 22 PHE 0.017 0.001 PHE D 94 TYR 0.010 0.001 TYR E 214 ARG 0.002 0.000 ARG A 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 192 time to evaluate : 0.846 Fit side-chains REVERT: A 45 TYR cc_start: 0.8248 (m-80) cc_final: 0.7870 (m-80) REVERT: A 63 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8909 (mm) REVERT: A 158 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.9122 (m-80) REVERT: A 220 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8498 (mt) REVERT: C 40 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.8871 (p) REVERT: C 43 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7464 (pp20) REVERT: C 45 TYR cc_start: 0.8209 (m-80) cc_final: 0.7763 (m-80) REVERT: C 73 MET cc_start: 0.6325 (tpt) cc_final: 0.6100 (tpt) REVERT: C 158 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.9099 (m-80) REVERT: C 220 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8525 (mt) REVERT: D 45 TYR cc_start: 0.8255 (m-80) cc_final: 0.7950 (m-80) REVERT: D 49 TYR cc_start: 0.8092 (t80) cc_final: 0.7862 (t80) REVERT: D 63 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8934 (mm) REVERT: D 158 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.9062 (m-80) REVERT: D 220 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8501 (mt) REVERT: E 43 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: E 63 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9137 (mm) REVERT: E 158 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.9051 (m-80) REVERT: E 220 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8559 (mt) outliers start: 77 outliers final: 61 residues processed: 245 average time/residue: 0.1458 time to fit residues: 51.7693 Evaluate side-chains 264 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 189 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 85 PHE Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.124005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098949 restraints weight = 15722.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.102310 restraints weight = 6967.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104477 restraints weight = 4289.995| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8244 Z= 0.191 Angle : 0.724 12.192 11112 Z= 0.346 Chirality : 0.043 0.175 1260 Planarity : 0.003 0.025 1272 Dihedral : 16.772 105.840 1516 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 8.82 % Allowed : 31.37 % Favored : 59.80 % 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: -0.14 (0.28), residues: 896 helix: 0.58 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -2.26 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 54 HIS 0.001 0.000 HIS E 22 PHE 0.017 0.001 PHE A 94 TYR 0.010 0.001 TYR D 214 ARG 0.002 0.000 ARG A 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.33 seconds wall clock time: 31 minutes 27.55 seconds (1887.55 seconds total)