Starting phenix.real_space_refine on Sat Mar 16 13:40:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/03_2024/8ouz_17206_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/03_2024/8ouz_17206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/03_2024/8ouz_17206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/03_2024/8ouz_17206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/03_2024/8ouz_17206_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/03_2024/8ouz_17206_trim_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 49 5.16 5 C 4603 2.51 5 N 1267 2.21 5 O 1519 1.98 5 H 7373 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14822 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1132 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "B" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4960 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 2 Chain: "C" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4722 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 7, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3774 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Time building chain proxies: 6.82, per 1000 atoms: 0.46 Number of scatterers: 14822 At special positions: 0 Unit cell: (93.7125, 103.275, 93.7125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 8 15.00 Mg 3 11.99 O 1519 8.00 N 1267 7.00 C 4603 6.00 H 7373 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.33 Conformation dependent library (CDL) restraints added in 1.4 seconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 4 sheets defined 44.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 No H-bonds generated for 'chain 'A' and resid 6 through 9' Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.965A pdb=" N HIS A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 31 Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.664A pdb=" N ALA A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 105 through 111 Processing helix chain 'B' and resid 131 through 143 removed outlier: 4.388A pdb=" N GLN B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 166 through 186 removed outlier: 3.595A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 removed outlier: 3.887A pdb=" N ASP B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 removed outlier: 3.666A pdb=" N HIS B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 232 Proline residue: B 227 - end of helix removed outlier: 3.811A pdb=" N GLU B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 267 through 275 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 47 through 61 Processing helix chain 'C' and resid 68 through 78 removed outlier: 3.715A pdb=" N THR C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 157 through 164 Processing helix chain 'C' and resid 175 through 191 Processing helix chain 'C' and resid 208 through 215 Proline residue: C 214 - end of helix Processing helix chain 'C' and resid 222 through 239 Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.804A pdb=" N PHE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 270' Processing helix chain 'D' and resid 24 through 27 No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 54 through 66 Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 89 through 99 Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.886A pdb=" N ARG D 114 " --> pdb=" O TYR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.985A pdb=" N GLU D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 Processing helix chain 'D' and resid 166 through 169 No H-bonds generated for 'chain 'D' and resid 166 through 169' Processing helix chain 'D' and resid 171 through 186 Processing helix chain 'D' and resid 229 through 234 removed outlier: 4.071A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 336 through 338 removed outlier: 6.644A pdb=" N ARG B 312 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 280 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE B 123 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU B 282 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU B 154 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL B 239 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 156 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL B 241 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 158 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 340 through 342 Processing sheet with id= C, first strand: chain 'C' and resid 306 through 309 removed outlier: 6.230A pdb=" N ARG C 275 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 245 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE C 105 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 247 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 276 through 279 removed outlier: 3.548A pdb=" N HIS D 237 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY D 48 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N GLU D 77 " --> pdb=" O CYS D 144 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU D 146 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU D 79 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 148 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 81 " --> pdb=" O LEU D 148 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 870 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: 5.40 Time building geometry restraints manager: 12.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7345 1.03 - 1.23: 31 1.23 - 1.42: 2984 1.42 - 1.62: 4363 1.62 - 1.81: 70 Bond restraints: 14793 Sorted by residual: bond pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.43e+00 bond pdb=" N GLY C 2 " pdb=" CA GLY C 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.96e+00 bond pdb=" N GLN B 11 " pdb=" CA GLN B 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N LYS A 4 " pdb=" CA LYS A 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N GLY D 20 " pdb=" H GLY D 20 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 14788 not shown) Histogram of bond angle deviations from ideal: 100.46 - 108.33: 4275 108.33 - 116.20: 15242 116.20 - 124.07: 6276 124.07 - 131.94: 947 131.94 - 139.80: 14 Bond angle restraints: 26754 Sorted by residual: angle pdb=" C3' ATP D 301 " pdb=" C2' ATP D 301 " pdb=" O2' ATP D 301 " ideal model delta sigma weight residual 111.83 104.67 7.16 2.67e+00 1.40e-01 7.20e+00 angle pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " pdb=" C5' ATP C 401 " ideal model delta sigma weight residual 115.19 110.70 4.49 1.76e+00 3.23e-01 6.50e+00 angle pdb=" C3' ATP D 301 " pdb=" C4' ATP D 301 " pdb=" C5' ATP D 301 " ideal model delta sigma weight residual 115.19 110.75 4.44 1.76e+00 3.23e-01 6.37e+00 angle pdb=" C2' ATP D 301 " pdb=" C3' ATP D 301 " pdb=" O3' ATP D 301 " ideal model delta sigma weight residual 111.83 105.24 6.59 2.67e+00 1.40e-01 6.10e+00 angle pdb=" C3' ATP D 301 " pdb=" C4' ATP D 301 " pdb=" O4' ATP D 301 " ideal model delta sigma weight residual 105.22 102.02 3.20 1.30e+00 5.94e-01 6.09e+00 ... (remaining 26749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.10: 6562 29.10 - 58.20: 311 58.20 - 87.29: 34 87.29 - 116.39: 3 116.39 - 145.49: 1 Dihedral angle restraints: 6911 sinusoidal: 3876 harmonic: 3035 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.49 -145.49 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -171.86 111.86 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 36.74 -96.74 1 2.00e+01 2.50e-03 2.68e+01 ... (remaining 6908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1042 0.060 - 0.119: 111 0.119 - 0.179: 17 0.179 - 0.239: 0 0.239 - 0.298: 6 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C2' ATP D 301 " pdb=" C1' ATP D 301 " pdb=" C3' ATP D 301 " pdb=" O2' ATP D 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ATP D 301 " pdb=" C2' ATP D 301 " pdb=" C4' ATP D 301 " pdb=" O3' ATP D 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' ATP C 401 " pdb=" C1' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O2' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1173 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 34 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO A 35 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 307 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" CD GLU C 307 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU C 307 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU C 307 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 263 " -0.005 2.00e-02 2.50e+03 9.70e-03 9.41e-01 pdb=" C ASN B 263 " 0.017 2.00e-02 2.50e+03 pdb=" O ASN B 263 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY B 264 " -0.006 2.00e-02 2.50e+03 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 392 2.13 - 2.75: 27133 2.75 - 3.37: 42432 3.37 - 3.98: 55325 3.98 - 4.60: 86968 Nonbonded interactions: 212250 Sorted by model distance: nonbonded pdb=" HG1 THR B 132 " pdb="MG MG B 402 " model vdw 1.513 1.700 nonbonded pdb=" OE1 GLN D 200 " pdb=" H GLN D 200 " model vdw 1.534 1.850 nonbonded pdb=" HG1 THR D 55 " pdb="MG MG D 302 " model vdw 1.548 1.700 nonbonded pdb=" O ILE D 66 " pdb="HH21 ARG D 114 " model vdw 1.652 1.850 nonbonded pdb=" OE1 GLU C 104 " pdb="HH11 ARG C 275 " model vdw 1.652 1.850 ... (remaining 212245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.250 Extract box with map and model: 7.190 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 51.010 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7420 Z= 0.174 Angle : 0.561 7.161 10033 Z= 0.290 Chirality : 0.044 0.298 1176 Planarity : 0.003 0.031 1256 Dihedral : 16.592 145.487 2805 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.00 % Allowed : 12.84 % Favored : 86.16 % 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: 1.04 (0.28), residues: 906 helix: 1.66 (0.26), residues: 423 sheet: 0.45 (0.41), residues: 163 loop : -0.43 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.004 0.001 HIS B 179 PHE 0.010 0.001 PHE C 176 TYR 0.009 0.001 TYR D 119 ARG 0.006 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 100 average time/residue: 2.8744 time to fit residues: 302.2520 Evaluate side-chains 88 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7420 Z= 0.266 Angle : 0.561 7.442 10033 Z= 0.292 Chirality : 0.041 0.141 1176 Planarity : 0.004 0.043 1256 Dihedral : 10.364 123.649 1077 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.24 % Allowed : 12.84 % Favored : 84.91 % 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: 0.70 (0.28), residues: 906 helix: 1.30 (0.25), residues: 425 sheet: 0.36 (0.41), residues: 165 loop : -0.52 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 268 HIS 0.004 0.001 HIS D 60 PHE 0.013 0.002 PHE D 80 TYR 0.011 0.002 TYR D 155 ARG 0.007 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 224 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.5931 (ttt180) outliers start: 18 outliers final: 11 residues processed: 104 average time/residue: 2.5568 time to fit residues: 281.6361 Evaluate side-chains 98 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 224 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7420 Z= 0.210 Angle : 0.523 6.973 10033 Z= 0.269 Chirality : 0.039 0.136 1176 Planarity : 0.003 0.035 1256 Dihedral : 9.935 95.398 1076 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.12 % Allowed : 13.47 % Favored : 84.41 % 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: 0.74 (0.28), residues: 906 helix: 1.40 (0.25), residues: 425 sheet: 0.27 (0.41), residues: 165 loop : -0.54 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 268 HIS 0.003 0.001 HIS D 60 PHE 0.011 0.001 PHE D 80 TYR 0.009 0.001 TYR B 210 ARG 0.004 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 224 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.5894 (ttt180) outliers start: 17 outliers final: 9 residues processed: 103 average time/residue: 2.6074 time to fit residues: 283.8241 Evaluate side-chains 98 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 224 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7420 Z= 0.211 Angle : 0.527 6.785 10033 Z= 0.271 Chirality : 0.039 0.136 1176 Planarity : 0.003 0.035 1256 Dihedral : 9.307 88.800 1073 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.24 % Allowed : 13.59 % Favored : 84.16 % 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: 0.76 (0.28), residues: 906 helix: 1.42 (0.26), residues: 425 sheet: 0.29 (0.41), residues: 165 loop : -0.54 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 268 HIS 0.003 0.001 HIS D 237 PHE 0.012 0.001 PHE D 80 TYR 0.009 0.001 TYR B 210 ARG 0.004 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 192 GLN cc_start: 0.6480 (pp30) cc_final: 0.6261 (pp30) REVERT: D 187 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: D 224 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.5898 (ttt180) outliers start: 18 outliers final: 13 residues processed: 104 average time/residue: 2.5710 time to fit residues: 282.9028 Evaluate side-chains 102 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 224 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7420 Z= 0.235 Angle : 0.545 7.023 10033 Z= 0.280 Chirality : 0.040 0.137 1176 Planarity : 0.004 0.036 1256 Dihedral : 9.100 88.258 1073 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.87 % Allowed : 13.97 % Favored : 83.17 % 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: 0.69 (0.28), residues: 906 helix: 1.35 (0.25), residues: 424 sheet: 0.27 (0.41), residues: 165 loop : -0.57 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 314 HIS 0.004 0.001 HIS D 237 PHE 0.012 0.001 PHE D 80 TYR 0.010 0.001 TYR D 155 ARG 0.004 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 187 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: D 224 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.5863 (ttt180) REVERT: D 239 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7861 (mtt) outliers start: 23 outliers final: 13 residues processed: 109 average time/residue: 2.5770 time to fit residues: 297.4817 Evaluate side-chains 104 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7420 Z= 0.205 Angle : 0.530 6.450 10033 Z= 0.271 Chirality : 0.039 0.135 1176 Planarity : 0.003 0.036 1256 Dihedral : 8.889 89.673 1073 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.24 % Allowed : 14.21 % Favored : 83.54 % 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: 0.74 (0.28), residues: 906 helix: 1.41 (0.26), residues: 425 sheet: 0.27 (0.41), residues: 165 loop : -0.56 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 268 HIS 0.003 0.001 HIS D 237 PHE 0.011 0.001 PHE D 80 TYR 0.009 0.001 TYR B 210 ARG 0.005 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 196 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7851 (mt) REVERT: D 187 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: D 224 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.5861 (ttt180) REVERT: D 239 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7865 (mtt) outliers start: 18 outliers final: 11 residues processed: 101 average time/residue: 2.5050 time to fit residues: 268.1652 Evaluate side-chains 101 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7420 Z= 0.202 Angle : 0.528 6.229 10033 Z= 0.270 Chirality : 0.039 0.135 1176 Planarity : 0.003 0.035 1256 Dihedral : 8.736 89.395 1073 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.37 % Allowed : 14.34 % Favored : 83.29 % 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: 0.75 (0.28), residues: 906 helix: 1.43 (0.26), residues: 425 sheet: 0.27 (0.41), residues: 165 loop : -0.57 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 268 HIS 0.003 0.001 HIS D 237 PHE 0.011 0.001 PHE D 80 TYR 0.009 0.001 TYR B 210 ARG 0.005 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: B 196 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7853 (mt) REVERT: D 187 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: D 224 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.5862 (ttt180) REVERT: D 239 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7859 (mtt) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 2.6619 time to fit residues: 295.4683 Evaluate side-chains 102 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN D 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7420 Z= 0.217 Angle : 0.537 6.130 10033 Z= 0.276 Chirality : 0.039 0.136 1176 Planarity : 0.003 0.035 1256 Dihedral : 8.765 89.537 1073 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.49 % Allowed : 14.59 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.28), residues: 906 helix: 1.38 (0.25), residues: 425 sheet: 0.27 (0.41), residues: 165 loop : -0.60 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 314 HIS 0.004 0.001 HIS D 237 PHE 0.012 0.001 PHE D 80 TYR 0.010 0.001 TYR B 210 ARG 0.004 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: B 196 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7855 (mt) REVERT: D 187 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: D 224 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.5857 (ttt180) REVERT: D 239 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7881 (mtt) outliers start: 20 outliers final: 12 residues processed: 110 average time/residue: 2.6649 time to fit residues: 310.8837 Evaluate side-chains 106 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7420 Z= 0.156 Angle : 0.505 6.404 10033 Z= 0.257 Chirality : 0.038 0.133 1176 Planarity : 0.003 0.034 1256 Dihedral : 8.366 87.090 1073 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.75 % Allowed : 15.71 % Favored : 82.54 % 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: 0.93 (0.28), residues: 906 helix: 1.62 (0.26), residues: 425 sheet: 0.35 (0.41), residues: 163 loop : -0.54 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.003 0.001 HIS B 179 PHE 0.009 0.001 PHE C 176 TYR 0.008 0.001 TYR D 119 ARG 0.005 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: B 196 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7842 (mt) REVERT: C 38 GLU cc_start: 0.6691 (tm-30) cc_final: 0.6357 (tm-30) REVERT: C 184 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7700 (mt-10) REVERT: D 90 LEU cc_start: 0.8132 (tp) cc_final: 0.7904 (mp) REVERT: D 187 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.6614 (m-80) REVERT: D 224 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.5880 (ttt180) REVERT: D 239 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7793 (mtt) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 2.7005 time to fit residues: 278.9948 Evaluate side-chains 98 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7420 Z= 0.182 Angle : 0.521 6.394 10033 Z= 0.266 Chirality : 0.039 0.134 1176 Planarity : 0.003 0.034 1256 Dihedral : 8.386 87.486 1072 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.75 % Allowed : 15.71 % Favored : 82.54 % 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: 0.91 (0.28), residues: 906 helix: 1.59 (0.26), residues: 425 sheet: 0.32 (0.41), residues: 165 loop : -0.53 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 268 HIS 0.004 0.001 HIS B 179 PHE 0.011 0.001 PHE D 80 TYR 0.008 0.001 TYR B 210 ARG 0.005 0.000 ARG B 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: C 184 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7749 (mt-10) REVERT: D 90 LEU cc_start: 0.8146 (tp) cc_final: 0.7911 (mp) REVERT: D 187 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: D 224 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.5873 (ttt180) REVERT: D 239 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7789 (mtt) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 2.6585 time to fit residues: 268.8110 Evaluate side-chains 96 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.144340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114861 restraints weight = 24866.208| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.94 r_work: 0.3442 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7420 Z= 0.214 Angle : 0.541 6.299 10033 Z= 0.278 Chirality : 0.039 0.137 1176 Planarity : 0.003 0.035 1256 Dihedral : 8.403 89.529 1070 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.62 % Allowed : 15.84 % Favored : 82.54 % 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: 0.77 (0.28), residues: 906 helix: 1.49 (0.25), residues: 423 sheet: 0.30 (0.41), residues: 165 loop : -0.63 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 268 HIS 0.005 0.001 HIS B 179 PHE 0.012 0.001 PHE D 80 TYR 0.009 0.001 TYR B 210 ARG 0.004 0.000 ARG B 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6154.13 seconds wall clock time: 107 minutes 46.14 seconds (6466.14 seconds total)