Starting phenix.real_space_refine on Sun Mar 10 21:38:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cti_26991/03_2024/8cti_26991.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cti_26991/03_2024/8cti_26991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cti_26991/03_2024/8cti_26991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cti_26991/03_2024/8cti_26991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cti_26991/03_2024/8cti_26991.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cti_26991/03_2024/8cti_26991.pdb" } resolution = 3.6 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= 0.041 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 70 5.49 5 S 19 5.16 5 C 3114 2.51 5 N 916 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 45": "OD1" <-> "OD2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5297 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1658 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2131 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 3 Chain: "C" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1508 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 59} Time building chain proxies: 3.73, per 1000 atoms: 0.70 Number of scatterers: 5297 At special positions: 0 Unit cell: (69.3, 89.1, 118.8, 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 19 16.00 P 70 15.00 O 1178 8.00 N 916 7.00 C 3114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 686.5 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 8 sheets defined 19.2% alpha, 32.3% beta 23 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.927A pdb=" N GLU A 48 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 removed outlier: 3.641A pdb=" N VAL A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 125 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 168 through 174 removed outlier: 4.012A pdb=" N LYS A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 174 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 200 through 214 removed outlier: 3.775A pdb=" N HIS A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.742A pdb=" N LEU A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 138 removed outlier: 8.288A pdb=" N LEU A 137 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 105 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 102 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU A 79 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE A 158 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA A 81 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU A 160 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 83 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR A 155 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TYR A 195 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N MET A 157 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 197 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE A 159 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY A 192 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE A 255 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 69 removed outlier: 4.233A pdb=" N ALA B 66 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 97 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG B 89 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS B 95 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.587A pdb=" N ALA B 107 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 142 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER B 128 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU B 140 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.890A pdb=" N ALA B 163 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 151 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU B 161 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 172 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE B 169 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 183 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 171 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 196 removed outlier: 3.595A pdb=" N SER B 208 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU B 217 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN B 223 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 252 removed outlier: 3.682A pdb=" N ARG B 248 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 261 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS B 262 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL B 267 " --> pdb=" O CYS B 262 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 268 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN B 285 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 270 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 297 removed outlier: 3.701A pdb=" N ASP B 294 " --> pdb=" O LEU B 306 " (cutoff:3.500A) 123 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.00: 1 1.00 - 1.22: 8 1.22 - 1.44: 2670 1.44 - 1.66: 2861 1.66 - 1.87: 25 Bond restraints: 5565 Sorted by residual: bond pdb=" CG PRO B 134 " pdb=" CD PRO B 134 " ideal model delta sigma weight residual 1.503 0.783 0.720 3.40e-02 8.65e+02 4.49e+02 bond pdb=" CB PRO B 134 " pdb=" CG PRO B 134 " ideal model delta sigma weight residual 1.492 1.874 -0.382 5.00e-02 4.00e+02 5.83e+01 bond pdb=" N PRO B 134 " pdb=" CD PRO B 134 " ideal model delta sigma weight residual 1.473 1.561 -0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" CA PRO B 134 " pdb=" CB PRO B 134 " ideal model delta sigma weight residual 1.534 1.482 0.051 1.49e-02 4.50e+03 1.19e+01 bond pdb=" CB ASP A 45 " pdb=" CG ASP A 45 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.24e+00 ... (remaining 5560 not shown) Histogram of bond angle deviations from ideal: 72.13 - 84.51: 1 84.51 - 96.88: 3 96.88 - 109.26: 1235 109.26 - 121.64: 5306 121.64 - 134.01: 1338 Bond angle restraints: 7883 Sorted by residual: angle pdb=" N PRO B 134 " pdb=" CD PRO B 134 " pdb=" CG PRO B 134 " ideal model delta sigma weight residual 103.20 72.13 31.07 1.50e+00 4.44e-01 4.29e+02 angle pdb=" CA PRO B 134 " pdb=" CB PRO B 134 " pdb=" CG PRO B 134 " ideal model delta sigma weight residual 104.50 85.59 18.91 1.90e+00 2.77e-01 9.91e+01 angle pdb=" N PRO B 134 " pdb=" CA PRO B 134 " pdb=" CB PRO B 134 " ideal model delta sigma weight residual 103.33 94.12 9.21 1.10e+00 8.26e-01 7.01e+01 angle pdb=" CA PRO B 134 " pdb=" N PRO B 134 " pdb=" CD PRO B 134 " ideal model delta sigma weight residual 112.00 105.45 6.55 1.40e+00 5.10e-01 2.19e+01 angle pdb=" CB PRO B 134 " pdb=" CG PRO B 134 " pdb=" CD PRO B 134 " ideal model delta sigma weight residual 106.10 91.98 14.12 3.20e+00 9.77e-02 1.95e+01 ... (remaining 7878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 2942 22.15 - 44.30: 295 44.30 - 66.45: 147 66.45 - 88.60: 23 88.60 - 110.75: 1 Dihedral angle restraints: 3408 sinusoidal: 2037 harmonic: 1371 Sorted by residual: dihedral pdb=" O4' U C 19 " pdb=" C1' U C 19 " pdb=" N1 U C 19 " pdb=" C2 U C 19 " ideal model delta sinusoidal sigma weight residual 200.00 89.25 110.75 1 1.50e+01 4.44e-03 5.78e+01 dihedral pdb=" O4' C C 16 " pdb=" C1' C C 16 " pdb=" N1 C C 16 " pdb=" C2 C C 16 " ideal model delta sinusoidal sigma weight residual -128.00 -55.71 -72.29 1 1.70e+01 3.46e-03 2.31e+01 dihedral pdb=" O4' A C 7 " pdb=" C1' A C 7 " pdb=" N9 A C 7 " pdb=" C4 A C 7 " ideal model delta sinusoidal sigma weight residual -106.00 -170.80 64.80 1 1.70e+01 3.46e-03 1.91e+01 ... (remaining 3405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 750 0.043 - 0.085: 123 0.085 - 0.128: 59 0.128 - 0.170: 6 0.170 - 0.213: 1 Chirality restraints: 939 Sorted by residual: chirality pdb=" CA ASP A 45 " pdb=" N ASP A 45 " pdb=" C ASP A 45 " pdb=" CB ASP A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA GLN A 117 " pdb=" N GLN A 117 " pdb=" C GLN A 117 " pdb=" CB GLN A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CG LEU B 149 " pdb=" CB LEU B 149 " pdb=" CD1 LEU B 149 " pdb=" CD2 LEU B 149 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 936 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 133 " 0.053 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO B 134 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 134 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 134 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 118 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" CG ASP A 118 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 118 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 118 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 133 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C GLU B 133 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU B 133 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO B 134 " -0.012 2.00e-02 2.50e+03 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 300 2.71 - 3.26: 4875 3.26 - 3.81: 9539 3.81 - 4.35: 11728 4.35 - 4.90: 17905 Nonbonded interactions: 44347 Sorted by model distance: nonbonded pdb=" O2' G C 17 " pdb=" N2 G C 57 " model vdw 2.164 2.520 nonbonded pdb=" O GLY A 89 " pdb=" OG SER A 237 " model vdw 2.245 2.440 nonbonded pdb=" O LYS A 143 " pdb=" NZ LYS B 168 " model vdw 2.259 2.520 nonbonded pdb=" NH1 ARG A 258 " pdb=" O ILE A 259 " model vdw 2.274 2.520 nonbonded pdb=" O ASP A 45 " pdb=" OD1 ASP A 45 " model vdw 2.286 3.040 ... (remaining 44342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.020 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 20.340 Find NCS groups from input model: 0.120 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 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 : 0.011 0.720 5565 Z= 0.828 Angle : 0.792 31.069 7883 Z= 0.439 Chirality : 0.040 0.213 939 Planarity : 0.005 0.075 740 Dihedral : 20.285 110.750 2518 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.49 % Allowed : 22.87 % Favored : 76.64 % 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: -1.49 (0.38), residues: 459 helix: -1.33 (0.55), residues: 69 sheet: -0.36 (0.42), residues: 162 loop : -1.28 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 206 HIS 0.005 0.001 HIS B 187 PHE 0.016 0.002 PHE A 256 TYR 0.019 0.001 TYR B 38 ARG 0.002 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.469 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.1269 time to fit residues: 8.6314 Evaluate side-chains 38 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5565 Z= 0.301 Angle : 0.658 8.462 7883 Z= 0.335 Chirality : 0.042 0.152 939 Planarity : 0.005 0.033 740 Dihedral : 19.992 104.533 1631 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.38 % Allowed : 19.71 % Favored : 75.91 % 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: -1.15 (0.39), residues: 459 helix: -0.43 (0.57), residues: 70 sheet: -0.39 (0.41), residues: 169 loop : -1.09 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 252 HIS 0.006 0.002 HIS B 187 PHE 0.020 0.002 PHE A 256 TYR 0.017 0.002 TYR B 218 ARG 0.004 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.448 Fit side-chains REVERT: A 211 PHE cc_start: 0.4904 (OUTLIER) cc_final: 0.4653 (t80) REVERT: B 133 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7742 (tm-30) outliers start: 18 outliers final: 12 residues processed: 65 average time/residue: 0.1143 time to fit residues: 10.8404 Evaluate side-chains 54 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 156 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 10.0000 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5565 Z= 0.183 Angle : 0.541 8.533 7883 Z= 0.275 Chirality : 0.038 0.143 939 Planarity : 0.004 0.034 740 Dihedral : 19.709 102.223 1631 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.89 % Allowed : 22.14 % Favored : 73.97 % 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: -0.93 (0.39), residues: 459 helix: -0.07 (0.57), residues: 70 sheet: -0.28 (0.40), residues: 178 loop : -1.00 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.004 0.001 HIS B 187 PHE 0.020 0.002 PHE B 36 TYR 0.010 0.001 TYR B 218 ARG 0.003 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.483 Fit side-chains REVERT: A 211 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.4627 (t80) REVERT: B 133 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 187 HIS cc_start: 0.6077 (OUTLIER) cc_final: 0.5792 (m170) outliers start: 16 outliers final: 11 residues processed: 64 average time/residue: 0.1220 time to fit residues: 11.6174 Evaluate side-chains 57 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5565 Z= 0.187 Angle : 0.523 8.938 7883 Z= 0.265 Chirality : 0.038 0.136 939 Planarity : 0.004 0.035 740 Dihedral : 19.541 96.537 1631 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.35 % Allowed : 21.65 % Favored : 72.99 % 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: -0.62 (0.40), residues: 459 helix: 0.56 (0.59), residues: 70 sheet: -0.11 (0.41), residues: 168 loop : -0.90 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.004 0.001 HIS B 187 PHE 0.023 0.002 PHE B 36 TYR 0.010 0.001 TYR B 218 ARG 0.002 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 51 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5815 (mt) REVERT: B 133 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 187 HIS cc_start: 0.6199 (OUTLIER) cc_final: 0.5956 (m170) outliers start: 22 outliers final: 13 residues processed: 68 average time/residue: 0.1334 time to fit residues: 12.7526 Evaluate side-chains 60 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 45 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.0040 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.6398 ------------------------------------------------------------------------------- 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: 0.6608 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5565 Z= 0.335 Angle : 0.664 9.204 7883 Z= 0.340 Chirality : 0.042 0.157 939 Planarity : 0.005 0.042 740 Dihedral : 19.764 91.053 1631 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 6.57 % Allowed : 21.41 % Favored : 72.02 % 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: -0.99 (0.38), residues: 459 helix: 0.44 (0.61), residues: 66 sheet: -0.44 (0.39), residues: 173 loop : -1.10 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 206 HIS 0.007 0.001 HIS B 178 PHE 0.018 0.002 PHE B 190 TYR 0.012 0.002 TYR B 218 ARG 0.006 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 50 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.5919 (mt) REVERT: A 138 ARG cc_start: 0.5902 (OUTLIER) cc_final: 0.4279 (tmt170) REVERT: B 133 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7640 (tm-30) REVERT: B 295 VAL cc_start: 0.6302 (p) cc_final: 0.6047 (t) outliers start: 27 outliers final: 20 residues processed: 69 average time/residue: 0.1262 time to fit residues: 12.4163 Evaluate side-chains 69 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 297 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.6480 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5565 Z= 0.185 Angle : 0.543 9.356 7883 Z= 0.275 Chirality : 0.039 0.177 939 Planarity : 0.004 0.037 740 Dihedral : 19.575 86.828 1631 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.62 % Allowed : 24.57 % Favored : 70.80 % 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: -0.80 (0.39), residues: 459 helix: 0.51 (0.59), residues: 70 sheet: -0.31 (0.40), residues: 182 loop : -1.01 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.009 0.001 HIS B 187 PHE 0.014 0.002 PHE B 36 TYR 0.011 0.001 TYR B 218 ARG 0.002 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5799 (mt) REVERT: A 260 GLN cc_start: 0.7399 (pm20) cc_final: 0.7035 (mm-40) REVERT: B 133 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7536 (tm-30) outliers start: 19 outliers final: 12 residues processed: 69 average time/residue: 0.1478 time to fit residues: 13.8345 Evaluate side-chains 60 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.6705 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 5565 Z= 0.399 Angle : 0.711 9.496 7883 Z= 0.361 Chirality : 0.044 0.164 939 Planarity : 0.005 0.040 740 Dihedral : 19.848 84.592 1631 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.84 % Allowed : 23.11 % Favored : 71.05 % 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: -1.20 (0.39), residues: 459 helix: 0.25 (0.60), residues: 66 sheet: -0.57 (0.40), residues: 171 loop : -1.24 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 206 HIS 0.006 0.002 HIS B 187 PHE 0.025 0.002 PHE B 69 TYR 0.012 0.002 TYR A 186 ARG 0.005 0.001 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 52 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.5910 (mt) REVERT: B 133 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 167 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: B 226 CYS cc_start: 0.6005 (t) cc_final: 0.5523 (p) REVERT: B 307 GLN cc_start: 0.5438 (pt0) cc_final: 0.5048 (pm20) outliers start: 24 outliers final: 16 residues processed: 69 average time/residue: 0.1723 time to fit residues: 15.9570 Evaluate side-chains 68 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.6572 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5565 Z= 0.217 Angle : 0.582 9.549 7883 Z= 0.295 Chirality : 0.039 0.168 939 Planarity : 0.004 0.038 740 Dihedral : 19.643 86.041 1631 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.11 % Allowed : 23.84 % Favored : 71.05 % 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 (0.39), residues: 459 helix: 0.39 (0.60), residues: 66 sheet: -0.51 (0.39), residues: 180 loop : -1.11 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.006 0.001 HIS B 187 PHE 0.019 0.002 PHE B 251 TYR 0.009 0.001 TYR A 150 ARG 0.002 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 48 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5781 (mt) REVERT: B 133 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 167 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: B 277 ARG cc_start: 0.8257 (tpt170) cc_final: 0.7723 (tpp80) REVERT: B 307 GLN cc_start: 0.5378 (pt0) cc_final: 0.5011 (pm20) outliers start: 21 outliers final: 16 residues processed: 65 average time/residue: 0.1579 time to fit residues: 14.2961 Evaluate side-chains 62 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5565 Z= 0.406 Angle : 0.731 9.760 7883 Z= 0.371 Chirality : 0.045 0.242 939 Planarity : 0.005 0.045 740 Dihedral : 19.916 84.710 1631 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.84 % Allowed : 23.11 % Favored : 71.05 % 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: -1.24 (0.39), residues: 459 helix: 0.21 (0.61), residues: 66 sheet: -0.53 (0.40), residues: 168 loop : -1.31 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 206 HIS 0.006 0.002 HIS B 178 PHE 0.026 0.003 PHE B 69 TYR 0.013 0.002 TYR A 186 ARG 0.006 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 50 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5962 (mt) REVERT: B 133 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 167 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: B 226 CYS cc_start: 0.6145 (m) cc_final: 0.5752 (p) REVERT: B 307 GLN cc_start: 0.5740 (pt0) cc_final: 0.5381 (pm20) outliers start: 24 outliers final: 19 residues processed: 68 average time/residue: 0.1673 time to fit residues: 15.2357 Evaluate side-chains 68 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 47 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.0020 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5565 Z= 0.197 Angle : 0.586 9.440 7883 Z= 0.298 Chirality : 0.039 0.179 939 Planarity : 0.005 0.046 740 Dihedral : 19.633 86.155 1631 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.38 % Allowed : 25.06 % Favored : 70.56 % 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: -1.04 (0.39), residues: 459 helix: 0.42 (0.59), residues: 66 sheet: -0.48 (0.39), residues: 177 loop : -1.15 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 206 HIS 0.007 0.001 HIS B 225 PHE 0.014 0.002 PHE A 256 TYR 0.008 0.001 TYR A 150 ARG 0.003 0.000 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5800 (mt) REVERT: A 260 GLN cc_start: 0.7462 (mp10) cc_final: 0.7137 (mp10) REVERT: B 133 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7562 (tm-30) REVERT: B 167 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: B 254 GLN cc_start: 0.7506 (tt0) cc_final: 0.7104 (tm-30) REVERT: B 307 GLN cc_start: 0.5641 (pt0) cc_final: 0.5344 (pm20) outliers start: 18 outliers final: 16 residues processed: 63 average time/residue: 0.1593 time to fit residues: 13.4930 Evaluate side-chains 65 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 0.0030 chunk 34 optimal weight: 0.5980 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.210416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.161769 restraints weight = 7549.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.165822 restraints weight = 8452.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.167453 restraints weight = 5839.494| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5565 Z= 0.170 Angle : 0.561 9.311 7883 Z= 0.285 Chirality : 0.038 0.155 939 Planarity : 0.005 0.048 740 Dihedral : 19.463 85.344 1631 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.38 % Allowed : 24.57 % Favored : 71.05 % 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: -0.84 (0.40), residues: 459 helix: 0.57 (0.57), residues: 70 sheet: -0.15 (0.42), residues: 162 loop : -1.19 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 206 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.001 PHE A 252 TYR 0.007 0.001 TYR A 150 ARG 0.004 0.000 ARG B 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1363.19 seconds wall clock time: 25 minutes 25.16 seconds (1525.16 seconds total)