Starting phenix.real_space_refine on Wed Jan 17 20:36:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmr_16122/01_2024/8bmr_16122.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmr_16122/01_2024/8bmr_16122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmr_16122/01_2024/8bmr_16122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmr_16122/01_2024/8bmr_16122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmr_16122/01_2024/8bmr_16122.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmr_16122/01_2024/8bmr_16122.pdb" } resolution = 3.8 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= 0.004 sd= 0.078 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4087 2.51 5 N 1050 2.21 5 O 1167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 217": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6330 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2129 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2131 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 1 Chain: "C" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2070 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Time building chain proxies: 3.92, per 1000 atoms: 0.62 Number of scatterers: 6330 At special positions: 0 Unit cell: (82.782, 83.804, 116.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1167 8.00 N 1050 7.00 C 4087 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 1.4 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 59.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 removed outlier: 4.803A pdb=" N SER A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 78 through 85 removed outlier: 3.962A pdb=" N VAL A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.619A pdb=" N GLN A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 97' Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 146 through 160 removed outlier: 3.765A pdb=" N GLN A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.249A pdb=" N ALA A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.595A pdb=" N LEU A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.757A pdb=" N GLN B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 4.378A pdb=" N LEU B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.577A pdb=" N ALA B 96 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 117 through 133 Processing helix chain 'B' and resid 135 through 139 removed outlier: 4.028A pdb=" N ILE B 139 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 removed outlier: 5.855A pdb=" N SER B 147 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 161 removed outlier: 3.688A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 155 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.830A pdb=" N VAL B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.686A pdb=" N PHE B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 242 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.515A pdb=" N VAL C 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 38 Processing helix chain 'C' and resid 40 through 59 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.847A pdb=" N PHE C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 86 removed outlier: 4.133A pdb=" N ILE C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 108 through 127 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.833A pdb=" N LEU C 148 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 185 removed outlier: 3.732A pdb=" N ARG C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 191 through 197 removed outlier: 3.908A pdb=" N LYS C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 225 removed outlier: 4.177A pdb=" N VAL C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 245 through 261 removed outlier: 4.034A pdb=" N VAL C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 11 removed outlier: 3.866A pdb=" N ASN A 4 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 26 " --> pdb=" O PHE A 8 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS A 10 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER A 24 " --> pdb=" O HIS A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.198A pdb=" N ILE A 165 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE A 200 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 167 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 213 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN A 224 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 215 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 30 removed outlier: 6.337A pdb=" N ASP B 24 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER B 9 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.455A pdb=" N SER B 88 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 36 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU B 219 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2038 1.35 - 1.46: 1411 1.46 - 1.58: 2958 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 6457 Sorted by residual: bond pdb=" CA ILE C 247 " pdb=" C ILE C 247 " ideal model delta sigma weight residual 1.520 1.529 -0.009 8.80e-03 1.29e+04 1.08e+00 bond pdb=" CB ARG B 85 " pdb=" CG ARG B 85 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" CB GLU A 256 " pdb=" CG GLU A 256 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.45e-01 bond pdb=" CB GLU B 163 " pdb=" CG GLU B 163 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.28e-01 bond pdb=" CA GLU B 163 " pdb=" CB GLU B 163 " ideal model delta sigma weight residual 1.530 1.543 -0.014 1.58e-02 4.01e+03 7.36e-01 ... (remaining 6452 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.08: 151 106.08 - 113.06: 3541 113.06 - 120.04: 2270 120.04 - 127.02: 2705 127.02 - 134.00: 76 Bond angle restraints: 8743 Sorted by residual: angle pdb=" CA ARG B 85 " pdb=" CB ARG B 85 " pdb=" CG ARG B 85 " ideal model delta sigma weight residual 114.10 119.41 -5.31 2.00e+00 2.50e-01 7.06e+00 angle pdb=" N ASP B 170 " pdb=" CA ASP B 170 " pdb=" C ASP B 170 " ideal model delta sigma weight residual 110.53 107.16 3.37 1.29e+00 6.01e-01 6.81e+00 angle pdb=" C GLU A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.70e+00 angle pdb=" CA GLU B 163 " pdb=" CB GLU B 163 " pdb=" CG GLU B 163 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.41e+00 angle pdb=" CB MET C 118 " pdb=" CG MET C 118 " pdb=" SD MET C 118 " ideal model delta sigma weight residual 112.70 120.17 -7.47 3.00e+00 1.11e-01 6.21e+00 ... (remaining 8738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3497 18.00 - 35.99: 334 35.99 - 53.99: 41 53.99 - 71.98: 5 71.98 - 89.98: 3 Dihedral angle restraints: 3880 sinusoidal: 1556 harmonic: 2324 Sorted by residual: dihedral pdb=" CA LEU B 169 " pdb=" C LEU B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LEU B 98 " pdb=" C LEU B 98 " pdb=" N PHE B 99 " pdb=" CA PHE B 99 " ideal model delta harmonic sigma weight residual 180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PHE C 188 " pdb=" C PHE C 188 " pdb=" N ASN C 189 " pdb=" CA ASN C 189 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 599 0.030 - 0.060: 259 0.060 - 0.090: 88 0.090 - 0.120: 55 0.120 - 0.150: 8 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA ILE B 166 " pdb=" N ILE B 166 " pdb=" C ILE B 166 " pdb=" CB ILE B 166 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA VAL C 201 " pdb=" N VAL C 201 " pdb=" C VAL C 201 " pdb=" CB VAL C 201 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 6 " pdb=" N ILE A 6 " pdb=" C ILE A 6 " pdb=" CB ILE A 6 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1006 not shown) Planarity restraints: 1105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 270 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LYS A 270 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS A 270 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 271 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 231 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 232 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 20 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 21 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.024 5.00e-02 4.00e+02 ... (remaining 1102 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1023 2.76 - 3.30: 6407 3.30 - 3.83: 10046 3.83 - 4.37: 11065 4.37 - 4.90: 19194 Nonbonded interactions: 47735 Sorted by model distance: nonbonded pdb=" O VAL C 55 " pdb=" OG1 THR C 58 " model vdw 2.228 2.440 nonbonded pdb=" O PHE A 13 " pdb=" OG SER A 18 " model vdw 2.235 2.440 nonbonded pdb=" OG1 THR A 171 " pdb=" OE2 GLU A 206 " model vdw 2.273 2.440 nonbonded pdb=" OE1 GLN A 150 " pdb=" OG SER A 170 " model vdw 2.305 2.440 nonbonded pdb=" OE2 GLU A 111 " pdb=" NH1 ARG C 233 " model vdw 2.314 2.520 ... (remaining 47730 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 20.660 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 0.034 6457 Z= 0.172 Angle : 0.611 7.473 8743 Z= 0.312 Chirality : 0.042 0.150 1009 Planarity : 0.005 0.052 1105 Dihedral : 13.549 89.979 2378 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.31), residues: 798 helix: 0.68 (0.26), residues: 414 sheet: 0.19 (0.69), residues: 68 loop : -0.94 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 238 HIS 0.003 0.001 HIS A 10 PHE 0.012 0.001 PHE C 166 TYR 0.010 0.001 TYR A 248 ARG 0.005 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.741 Fit side-chains REVERT: A 133 MET cc_start: 0.8903 (mmm) cc_final: 0.8617 (mmt) REVERT: B 220 HIS cc_start: 0.7879 (m90) cc_final: 0.7352 (m90) REVERT: B 268 LEU cc_start: 0.9060 (mm) cc_final: 0.8850 (mm) REVERT: C 140 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8417 (tm-30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1512 time to fit residues: 28.2844 Evaluate side-chains 113 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 23 optimal weight: 0.0670 chunk 37 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 54 ASN B 196 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6457 Z= 0.165 Angle : 0.561 6.535 8743 Z= 0.281 Chirality : 0.042 0.154 1009 Planarity : 0.004 0.047 1105 Dihedral : 4.215 18.933 855 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.74 % Allowed : 11.05 % Favored : 87.21 % 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: 0.37 (0.31), residues: 798 helix: 1.12 (0.26), residues: 429 sheet: 0.28 (0.68), residues: 68 loop : -1.00 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 238 HIS 0.014 0.002 HIS A 10 PHE 0.021 0.001 PHE C 113 TYR 0.012 0.001 TYR C 251 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 0.764 Fit side-chains REVERT: B 184 MET cc_start: 0.8400 (ttm) cc_final: 0.7980 (ttp) REVERT: B 186 GLN cc_start: 0.8643 (tp40) cc_final: 0.8233 (tp40) REVERT: B 220 HIS cc_start: 0.7886 (m90) cc_final: 0.7289 (m90) REVERT: B 268 LEU cc_start: 0.9077 (mm) cc_final: 0.8845 (mm) REVERT: C 134 GLU cc_start: 0.8745 (mp0) cc_final: 0.8380 (mp0) REVERT: C 140 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8471 (tm-30) outliers start: 12 outliers final: 8 residues processed: 139 average time/residue: 0.1620 time to fit residues: 30.9794 Evaluate side-chains 128 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.0370 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6457 Z= 0.331 Angle : 0.624 8.422 8743 Z= 0.313 Chirality : 0.044 0.149 1009 Planarity : 0.004 0.048 1105 Dihedral : 4.373 18.235 855 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.49 % Allowed : 14.10 % Favored : 82.41 % 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: 0.28 (0.31), residues: 798 helix: 1.13 (0.26), residues: 429 sheet: 0.09 (0.67), residues: 68 loop : -1.15 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 128 HIS 0.008 0.001 HIS A 10 PHE 0.029 0.002 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.004 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.842 Fit side-chains REVERT: B 85 ARG cc_start: 0.8476 (tpt-90) cc_final: 0.8191 (tpt-90) REVERT: B 184 MET cc_start: 0.8589 (ttm) cc_final: 0.8251 (ttp) REVERT: B 220 HIS cc_start: 0.7889 (m90) cc_final: 0.7314 (m90) REVERT: B 268 LEU cc_start: 0.9196 (mm) cc_final: 0.8975 (mm) REVERT: C 134 GLU cc_start: 0.8712 (mp0) cc_final: 0.8313 (mp0) REVERT: C 140 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8419 (tm-30) outliers start: 24 outliers final: 19 residues processed: 137 average time/residue: 0.1562 time to fit residues: 29.2103 Evaluate side-chains 133 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6457 Z= 0.204 Angle : 0.562 8.492 8743 Z= 0.280 Chirality : 0.042 0.153 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.262 18.471 855 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.20 % Allowed : 17.15 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.31), residues: 798 helix: 1.25 (0.26), residues: 430 sheet: 0.16 (0.67), residues: 68 loop : -1.05 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.005 0.001 HIS B 141 PHE 0.028 0.001 PHE B 99 TYR 0.020 0.001 TYR C 251 ARG 0.001 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.822 Fit side-chains REVERT: A 195 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8866 (pp) REVERT: B 85 ARG cc_start: 0.8480 (tpt-90) cc_final: 0.8145 (tpt-90) REVERT: B 186 GLN cc_start: 0.8761 (tp40) cc_final: 0.8381 (tp40) REVERT: B 220 HIS cc_start: 0.7904 (m90) cc_final: 0.7321 (m90) REVERT: B 268 LEU cc_start: 0.9194 (mm) cc_final: 0.8977 (mm) REVERT: C 113 PHE cc_start: 0.8137 (t80) cc_final: 0.7627 (t80) REVERT: C 134 GLU cc_start: 0.8770 (mp0) cc_final: 0.8363 (mp0) REVERT: C 140 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8396 (tm-30) outliers start: 22 outliers final: 15 residues processed: 137 average time/residue: 0.1640 time to fit residues: 30.7203 Evaluate side-chains 134 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6457 Z= 0.241 Angle : 0.581 9.066 8743 Z= 0.289 Chirality : 0.042 0.153 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.279 18.507 855 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.78 % Allowed : 18.46 % Favored : 77.76 % 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: 0.47 (0.31), residues: 798 helix: 1.28 (0.26), residues: 430 sheet: 0.14 (0.67), residues: 68 loop : -1.06 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.006 0.001 HIS B 141 PHE 0.028 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.002 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8858 (pp) REVERT: B 85 ARG cc_start: 0.8485 (tpt-90) cc_final: 0.8122 (tpt-90) REVERT: B 220 HIS cc_start: 0.7898 (m90) cc_final: 0.7292 (m90) REVERT: C 113 PHE cc_start: 0.8238 (t80) cc_final: 0.7726 (t80) REVERT: C 134 GLU cc_start: 0.8790 (mp0) cc_final: 0.8355 (mp0) REVERT: C 140 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8489 (tm-30) outliers start: 26 outliers final: 17 residues processed: 141 average time/residue: 0.1639 time to fit residues: 31.2726 Evaluate side-chains 136 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6457 Z= 0.229 Angle : 0.583 9.829 8743 Z= 0.287 Chirality : 0.042 0.157 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.263 17.971 855 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.07 % Allowed : 19.33 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.31), residues: 798 helix: 1.30 (0.26), residues: 430 sheet: 0.10 (0.67), residues: 68 loop : -1.02 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.006 0.001 HIS B 141 PHE 0.027 0.001 PHE B 99 TYR 0.021 0.001 TYR C 251 ARG 0.008 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8871 (pp) REVERT: B 85 ARG cc_start: 0.8495 (tpt-90) cc_final: 0.8144 (tpt-90) REVERT: B 186 GLN cc_start: 0.8791 (tp40) cc_final: 0.8443 (tp40) REVERT: B 220 HIS cc_start: 0.7903 (m90) cc_final: 0.7381 (m90) REVERT: C 113 PHE cc_start: 0.8267 (t80) cc_final: 0.7814 (t80) REVERT: C 140 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8452 (tm-30) outliers start: 28 outliers final: 19 residues processed: 141 average time/residue: 0.1464 time to fit residues: 28.3773 Evaluate side-chains 135 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6457 Z= 0.178 Angle : 0.588 10.371 8743 Z= 0.285 Chirality : 0.042 0.172 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.212 18.232 855 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.63 % Allowed : 20.78 % Favored : 75.58 % 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: 0.55 (0.31), residues: 798 helix: 1.30 (0.26), residues: 431 sheet: 0.17 (0.68), residues: 68 loop : -0.92 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 238 HIS 0.006 0.001 HIS B 141 PHE 0.026 0.001 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.007 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8855 (pp) REVERT: B 85 ARG cc_start: 0.8477 (tpt-90) cc_final: 0.8121 (tpt-90) REVERT: C 113 PHE cc_start: 0.8243 (t80) cc_final: 0.7822 (t80) REVERT: C 116 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7221 (t80) REVERT: C 134 GLU cc_start: 0.8857 (mp0) cc_final: 0.8174 (mp0) REVERT: C 140 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8452 (tm-30) outliers start: 25 outliers final: 16 residues processed: 139 average time/residue: 0.1501 time to fit residues: 28.9194 Evaluate side-chains 136 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6457 Z= 0.286 Angle : 0.634 10.439 8743 Z= 0.313 Chirality : 0.044 0.166 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.374 18.957 855 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.34 % Allowed : 21.22 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.31), residues: 798 helix: 1.23 (0.26), residues: 431 sheet: 0.04 (0.66), residues: 68 loop : -0.99 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.006 0.001 HIS B 141 PHE 0.026 0.001 PHE B 99 TYR 0.022 0.001 TYR C 251 ARG 0.008 0.001 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8856 (pp) REVERT: B 270 MET cc_start: 0.8720 (mmt) cc_final: 0.8357 (mmt) REVERT: C 113 PHE cc_start: 0.8252 (t80) cc_final: 0.7815 (t80) REVERT: C 134 GLU cc_start: 0.8895 (mp0) cc_final: 0.8223 (mp0) REVERT: C 140 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8469 (tm-30) outliers start: 23 outliers final: 18 residues processed: 132 average time/residue: 0.1539 time to fit residues: 28.1385 Evaluate side-chains 134 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6457 Z= 0.244 Angle : 0.628 11.241 8743 Z= 0.308 Chirality : 0.043 0.169 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.338 18.646 855 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.20 % Allowed : 21.66 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.31), residues: 798 helix: 1.25 (0.26), residues: 431 sheet: 0.02 (0.66), residues: 68 loop : -0.98 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.006 0.001 HIS B 141 PHE 0.024 0.001 PHE B 99 TYR 0.024 0.001 TYR C 251 ARG 0.007 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8855 (pp) REVERT: B 85 ARG cc_start: 0.8515 (tpt-90) cc_final: 0.8259 (tpt-90) REVERT: B 186 GLN cc_start: 0.8797 (tp40) cc_final: 0.8456 (tp40) REVERT: B 270 MET cc_start: 0.8698 (mmt) cc_final: 0.8312 (mmt) REVERT: C 113 PHE cc_start: 0.8247 (t80) cc_final: 0.7827 (t80) REVERT: C 116 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7311 (t80) REVERT: C 134 GLU cc_start: 0.8881 (mp0) cc_final: 0.8226 (mp0) REVERT: C 140 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8472 (tm-30) outliers start: 22 outliers final: 18 residues processed: 133 average time/residue: 0.1534 time to fit residues: 28.3093 Evaluate side-chains 138 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6457 Z= 0.301 Angle : 0.668 11.542 8743 Z= 0.326 Chirality : 0.044 0.174 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.441 19.620 855 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.20 % Allowed : 21.80 % Favored : 75.00 % 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: 0.42 (0.31), residues: 798 helix: 1.26 (0.26), residues: 427 sheet: -0.09 (0.66), residues: 68 loop : -1.01 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 80 HIS 0.005 0.001 HIS B 141 PHE 0.026 0.002 PHE B 99 TYR 0.023 0.001 TYR C 251 ARG 0.007 0.001 ARG A 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8867 (pp) REVERT: B 85 ARG cc_start: 0.8523 (tpt-90) cc_final: 0.8275 (tpt-90) REVERT: B 186 GLN cc_start: 0.8829 (tp40) cc_final: 0.8484 (tp40) REVERT: B 270 MET cc_start: 0.8710 (mmt) cc_final: 0.8351 (mmt) REVERT: C 113 PHE cc_start: 0.8251 (t80) cc_final: 0.7825 (t80) REVERT: C 134 GLU cc_start: 0.8845 (mp0) cc_final: 0.8163 (mp0) REVERT: C 140 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8478 (tm-30) outliers start: 22 outliers final: 21 residues processed: 131 average time/residue: 0.1510 time to fit residues: 27.3417 Evaluate side-chains 137 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 26 optimal weight: 0.0070 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN B 266 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.159610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123949 restraints weight = 10598.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127333 restraints weight = 6572.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.129445 restraints weight = 4757.485| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6457 Z= 0.161 Angle : 0.623 11.680 8743 Z= 0.297 Chirality : 0.042 0.157 1009 Planarity : 0.004 0.049 1105 Dihedral : 4.180 18.662 855 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.62 % Allowed : 23.11 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.31), residues: 798 helix: 1.35 (0.26), residues: 431 sheet: 0.04 (0.66), residues: 68 loop : -0.92 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 238 HIS 0.005 0.001 HIS B 141 PHE 0.021 0.001 PHE B 99 TYR 0.025 0.001 TYR C 251 ARG 0.006 0.000 ARG A 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.13 seconds wall clock time: 29 minutes 10.09 seconds (1750.09 seconds total)