Starting phenix.real_space_refine on Tue Feb 13 14:36:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bms_16124/02_2024/8bms_16124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bms_16124/02_2024/8bms_16124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bms_16124/02_2024/8bms_16124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bms_16124/02_2024/8bms_16124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bms_16124/02_2024/8bms_16124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bms_16124/02_2024/8bms_16124_updated.pdb" } resolution = 2.6 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= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 4173 2.51 5 N 1080 2.21 5 O 1283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6570 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2133 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "B" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2183 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "C" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2118 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 4.81, per 1000 atoms: 0.73 Number of scatterers: 6570 At special positions: 0 Unit cell: (72.732, 75.24, 122.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 6 15.00 Mg 2 11.99 O 1283 8.00 N 1080 7.00 C 4173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.9 seconds 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 5 sheets defined 51.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 102 through 112 removed outlier: 4.453A pdb=" N GLY A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.815A pdb=" N LYS A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.537A pdb=" N ILE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 268 through 280 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 103 through 114 removed outlier: 4.464A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.721A pdb=" N ILE B 139 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU B 140 " --> pdb=" O ASP B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 136 through 140' Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 178 through 194 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 248 through 259 Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 21 through 37 removed outlier: 3.675A pdb=" N PHE C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 3.688A pdb=" N THR C 58 " --> pdb=" O TYR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 86 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 103 through 129 Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.513A pdb=" N THR C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) Proline residue: C 145 - end of helix Processing helix chain 'C' and resid 153 through 183 removed outlier: 4.165A pdb=" N VAL C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 193 through 224 Proline residue: C 202 - end of helix removed outlier: 5.227A pdb=" N VAL C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) Proline residue: C 206 - end of helix removed outlier: 3.558A pdb=" N SER C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 261 Proline residue: C 248 - end of helix removed outlier: 4.170A pdb=" N LEU C 254 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU C 255 " --> pdb=" O CYS C 252 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 Processing sheet with id= B, first strand: chain 'A' and resid 220 through 225 removed outlier: 6.955A pdb=" N VAL A 215 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN A 224 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 213 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 197 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 38 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY A 40 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 28 through 30 Processing sheet with id= D, first strand: chain 'B' and resid 222 through 227 removed outlier: 6.768A pdb=" N ALA B 217 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS B 226 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 215 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 198 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU B 38 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU B 200 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLY B 40 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.285A pdb=" N TYR B 12 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE B 21 " --> pdb=" O TYR B 12 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 843 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: 1.77 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2078 1.34 - 1.46: 1013 1.46 - 1.57: 3479 1.57 - 1.69: 10 1.69 - 1.81: 50 Bond restraints: 6630 Sorted by residual: bond pdb=" CB ASN B 7 " pdb=" CG ASN B 7 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.83e+00 bond pdb=" CG1 ILE C 49 " pdb=" CD1 ILE C 49 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.51e+00 bond pdb=" CA ASN B 7 " pdb=" CB ASN B 7 " ideal model delta sigma weight residual 1.529 1.542 -0.013 1.58e-02 4.01e+03 6.59e-01 bond pdb=" C VAL C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 1.337 1.344 -0.007 9.80e-03 1.04e+04 5.69e-01 bond pdb=" CG1 ILE A 88 " pdb=" CD1 ILE A 88 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.60e-01 ... (remaining 6625 not shown) Histogram of bond angle deviations from ideal: 98.53 - 106.81: 216 106.81 - 115.10: 4081 115.10 - 123.38: 4481 123.38 - 131.66: 197 131.66 - 139.95: 19 Bond angle restraints: 8994 Sorted by residual: angle pdb=" CA MET C 118 " pdb=" CB MET C 118 " pdb=" CG MET C 118 " ideal model delta sigma weight residual 114.10 108.83 5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" CA ASN B 7 " pdb=" CB ASN B 7 " pdb=" CG ASN B 7 " ideal model delta sigma weight residual 112.60 114.79 -2.19 1.00e+00 1.00e+00 4.82e+00 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 108.88 113.61 -4.73 2.16e+00 2.14e-01 4.79e+00 angle pdb=" CA VAL C 201 " pdb=" C VAL C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 118.88 122.22 -3.34 1.54e+00 4.22e-01 4.70e+00 angle pdb=" N PHE A 231 " pdb=" CA PHE A 231 " pdb=" C PHE A 231 " ideal model delta sigma weight residual 109.81 114.54 -4.73 2.21e+00 2.05e-01 4.58e+00 ... (remaining 8989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 3608 17.47 - 34.94: 311 34.94 - 52.41: 77 52.41 - 69.88: 13 69.88 - 87.35: 10 Dihedral angle restraints: 4019 sinusoidal: 1654 harmonic: 2365 Sorted by residual: dihedral pdb=" CA ARG B 84 " pdb=" C ARG B 84 " pdb=" N ARG B 85 " pdb=" CA ARG B 85 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CG ARG C 182 " pdb=" CD ARG C 182 " pdb=" NE ARG C 182 " pdb=" CZ ARG C 182 " ideal model delta sinusoidal sigma weight residual 180.00 137.23 42.77 2 1.50e+01 4.44e-03 9.84e+00 dihedral pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " pdb=" CD GLU B 32 " pdb=" OE1 GLU B 32 " ideal model delta sinusoidal sigma weight residual 0.00 84.98 -84.98 1 3.00e+01 1.11e-03 9.73e+00 ... (remaining 4016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 644 0.029 - 0.059: 225 0.059 - 0.088: 98 0.088 - 0.117: 55 0.117 - 0.147: 12 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CA ILE B 167 " pdb=" N ILE B 167 " pdb=" C ILE B 167 " pdb=" CB ILE B 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE A 200 " pdb=" N ILE A 200 " pdb=" C ILE A 200 " pdb=" CB ILE A 200 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA MET C 118 " pdb=" N MET C 118 " pdb=" C MET C 118 " pdb=" CB MET C 118 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1031 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 231 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO A 232 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 110 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 111 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 72 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO B 73 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 73 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 73 " 0.022 5.00e-02 4.00e+02 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 55 2.55 - 3.13: 5098 3.13 - 3.72: 10553 3.72 - 4.31: 15445 4.31 - 4.90: 25505 Nonbonded interactions: 56656 Sorted by model distance: nonbonded pdb=" O2B ATP A 301 " pdb="MG MG A 302 " model vdw 1.956 2.170 nonbonded pdb=" OG SER B 47 " pdb="MG MG B 302 " model vdw 1.958 2.170 nonbonded pdb=" OE1 GLN A 91 " pdb="MG MG A 302 " model vdw 1.991 2.170 nonbonded pdb=" OE1 GLN B 92 " pdb="MG MG B 302 " model vdw 2.028 2.170 nonbonded pdb=" OG SER A 47 " pdb="MG MG A 302 " model vdw 2.043 2.170 ... (remaining 56651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.080 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: 0.000 Extract box with map and model: 24.050 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.840 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 0.048 6630 Z= 0.174 Angle : 0.522 7.334 8994 Z= 0.270 Chirality : 0.041 0.147 1034 Planarity : 0.004 0.057 1127 Dihedral : 14.825 87.345 2491 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.83 (0.29), residues: 814 helix: 1.57 (0.25), residues: 452 sheet: -0.80 (0.52), residues: 74 loop : -0.66 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.002 0.000 HIS A 10 PHE 0.011 0.001 PHE C 50 TYR 0.008 0.001 TYR B 162 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.764 Fit side-chains REVERT: A 180 GLU cc_start: 0.7829 (tt0) cc_final: 0.7373 (tt0) REVERT: A 184 ASP cc_start: 0.8172 (m-30) cc_final: 0.7873 (m-30) REVERT: C 106 LEU cc_start: 0.5436 (tt) cc_final: 0.4988 (tm) outliers start: 0 outliers final: 1 residues processed: 114 average time/residue: 1.1695 time to fit residues: 140.3824 Evaluate side-chains 91 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6630 Z= 0.289 Angle : 0.553 6.875 8994 Z= 0.278 Chirality : 0.043 0.151 1034 Planarity : 0.005 0.058 1127 Dihedral : 10.372 85.756 941 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.86 % Allowed : 7.43 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 814 helix: 1.45 (0.24), residues: 454 sheet: -0.79 (0.52), residues: 74 loop : -0.60 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.006 0.001 HIS A 10 PHE 0.012 0.001 PHE B 93 TYR 0.011 0.001 TYR B 162 ARG 0.002 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.797 Fit side-chains REVERT: A 62 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7673 (mm) REVERT: A 180 GLU cc_start: 0.7824 (tt0) cc_final: 0.7386 (tt0) REVERT: A 184 ASP cc_start: 0.8188 (m-30) cc_final: 0.7857 (m-30) REVERT: A 218 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: A 264 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: C 208 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.5983 (t80) REVERT: C 231 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6995 (tm-30) outliers start: 20 outliers final: 6 residues processed: 98 average time/residue: 1.1908 time to fit residues: 122.9553 Evaluate side-chains 101 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 77 ASN B 226 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6630 Z= 0.230 Angle : 0.514 7.225 8994 Z= 0.260 Chirality : 0.042 0.154 1034 Planarity : 0.004 0.057 1127 Dihedral : 9.991 85.998 939 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.71 % Allowed : 10.71 % Favored : 87.57 % 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: 0.88 (0.29), residues: 814 helix: 1.55 (0.25), residues: 453 sheet: -0.79 (0.52), residues: 74 loop : -0.53 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.005 0.001 HIS A 10 PHE 0.010 0.001 PHE A 231 TYR 0.010 0.001 TYR B 162 ARG 0.002 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.803 Fit side-chains REVERT: A 62 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7705 (mm) REVERT: A 173 MET cc_start: 0.8990 (mtm) cc_final: 0.8740 (mtt) REVERT: A 180 GLU cc_start: 0.7818 (tt0) cc_final: 0.7383 (tt0) REVERT: A 184 ASP cc_start: 0.8145 (m-30) cc_final: 0.7803 (m-30) REVERT: A 264 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: C 208 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.6008 (t80) outliers start: 12 outliers final: 4 residues processed: 90 average time/residue: 1.4822 time to fit residues: 140.2734 Evaluate side-chains 91 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6630 Z= 0.266 Angle : 0.534 7.100 8994 Z= 0.268 Chirality : 0.043 0.153 1034 Planarity : 0.005 0.058 1127 Dihedral : 10.054 87.206 939 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.29 % Allowed : 11.43 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.29), residues: 814 helix: 1.48 (0.25), residues: 453 sheet: -0.76 (0.52), residues: 74 loop : -0.48 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.006 0.001 HIS A 10 PHE 0.011 0.001 PHE B 116 TYR 0.011 0.001 TYR B 162 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.823 Fit side-chains REVERT: A 62 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7726 (mm) REVERT: A 173 MET cc_start: 0.9000 (mtm) cc_final: 0.8766 (mtt) REVERT: A 180 GLU cc_start: 0.7817 (tt0) cc_final: 0.7410 (tt0) REVERT: A 184 ASP cc_start: 0.8181 (m-30) cc_final: 0.7844 (m-30) REVERT: A 264 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: C 87 MET cc_start: 0.4700 (ptp) cc_final: 0.4169 (pp-130) REVERT: C 208 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.6022 (t80) REVERT: C 231 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6956 (tm-30) outliers start: 16 outliers final: 8 residues processed: 92 average time/residue: 1.3221 time to fit residues: 128.4187 Evaluate side-chains 95 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 6630 Z= 0.357 Angle : 0.590 7.070 8994 Z= 0.295 Chirality : 0.045 0.154 1034 Planarity : 0.005 0.058 1127 Dihedral : 10.401 86.939 939 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.00 % Allowed : 11.43 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.29), residues: 814 helix: 1.27 (0.24), residues: 453 sheet: -0.74 (0.52), residues: 74 loop : -0.52 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.006 0.001 HIS A 10 PHE 0.015 0.002 PHE B 93 TYR 0.014 0.001 TYR B 162 ARG 0.003 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.835 Fit side-chains REVERT: A 62 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7709 (mm) REVERT: A 173 MET cc_start: 0.8996 (mtm) cc_final: 0.8793 (mtt) REVERT: A 180 GLU cc_start: 0.7839 (tt0) cc_final: 0.7447 (tt0) REVERT: A 184 ASP cc_start: 0.8164 (m-30) cc_final: 0.7885 (m-30) REVERT: A 264 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: B 6 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7062 (pp20) REVERT: C 52 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6860 (mt) REVERT: C 87 MET cc_start: 0.4630 (ptp) cc_final: 0.4093 (pp-130) REVERT: C 208 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.6062 (t80) REVERT: C 231 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6898 (tm-30) outliers start: 21 outliers final: 8 residues processed: 97 average time/residue: 1.3821 time to fit residues: 140.7283 Evaluate side-chains 102 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 36 optimal weight: 0.0570 chunk 6 optimal weight: 0.0030 chunk 25 optimal weight: 0.0470 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 7 ASN B 243 HIS C 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6630 Z= 0.142 Angle : 0.474 7.329 8994 Z= 0.240 Chirality : 0.040 0.153 1034 Planarity : 0.004 0.056 1127 Dihedral : 9.502 84.832 939 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.00 % Allowed : 13.14 % Favored : 84.86 % 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: 1.07 (0.30), residues: 814 helix: 1.74 (0.25), residues: 452 sheet: -0.79 (0.52), residues: 74 loop : -0.48 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.006 0.001 HIS A 10 PHE 0.007 0.001 PHE C 50 TYR 0.005 0.001 TYR B 162 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.850 Fit side-chains REVERT: A 173 MET cc_start: 0.8978 (mtm) cc_final: 0.8717 (mtt) REVERT: A 180 GLU cc_start: 0.7807 (tt0) cc_final: 0.7425 (tt0) REVERT: A 184 ASP cc_start: 0.8144 (m-30) cc_final: 0.7851 (m-30) REVERT: A 264 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: B 214 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7439 (t70) REVERT: C 87 MET cc_start: 0.4624 (ptp) cc_final: 0.4118 (pp-130) REVERT: C 208 PHE cc_start: 0.6475 (OUTLIER) cc_final: 0.6021 (t80) REVERT: C 231 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6863 (tm-30) outliers start: 14 outliers final: 4 residues processed: 91 average time/residue: 1.1986 time to fit residues: 115.1672 Evaluate side-chains 94 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.0070 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.0020 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 7 ASN B 243 HIS C 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6630 Z= 0.181 Angle : 0.496 9.777 8994 Z= 0.248 Chirality : 0.041 0.168 1034 Planarity : 0.004 0.057 1127 Dihedral : 9.542 87.810 939 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.43 % Allowed : 13.43 % Favored : 84.14 % 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: 1.10 (0.29), residues: 814 helix: 1.75 (0.25), residues: 452 sheet: -0.74 (0.52), residues: 74 loop : -0.45 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.005 0.001 HIS A 10 PHE 0.012 0.001 PHE C 50 TYR 0.007 0.001 TYR B 162 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.783 Fit side-chains REVERT: A 173 MET cc_start: 0.8986 (mtm) cc_final: 0.8727 (mtt) REVERT: A 180 GLU cc_start: 0.7804 (tt0) cc_final: 0.7417 (tt0) REVERT: A 184 ASP cc_start: 0.8157 (m-30) cc_final: 0.7867 (m-30) REVERT: A 264 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: B 6 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7042 (pp20) REVERT: C 87 MET cc_start: 0.4613 (ptp) cc_final: 0.4114 (pp-130) REVERT: C 208 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.6070 (t80) REVERT: C 231 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6890 (tm-30) outliers start: 17 outliers final: 5 residues processed: 94 average time/residue: 1.2095 time to fit residues: 119.7691 Evaluate side-chains 94 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 7 ASN B 243 HIS C 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6630 Z= 0.319 Angle : 0.587 14.697 8994 Z= 0.288 Chirality : 0.044 0.222 1034 Planarity : 0.005 0.058 1127 Dihedral : 10.167 87.343 939 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.00 % Allowed : 13.86 % Favored : 84.14 % 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: 0.79 (0.29), residues: 814 helix: 1.42 (0.25), residues: 453 sheet: -0.67 (0.53), residues: 74 loop : -0.51 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.006 0.001 HIS A 10 PHE 0.016 0.002 PHE B 93 TYR 0.012 0.001 TYR B 162 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.802 Fit side-chains REVERT: A 62 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 180 GLU cc_start: 0.7839 (tt0) cc_final: 0.7435 (tt0) REVERT: A 184 ASP cc_start: 0.8164 (m-30) cc_final: 0.7851 (m-30) REVERT: A 264 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: B 6 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7057 (pp20) REVERT: C 87 MET cc_start: 0.4594 (ptp) cc_final: 0.4109 (pp-130) REVERT: C 208 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.6081 (t80) REVERT: C 231 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6899 (tm-30) outliers start: 14 outliers final: 6 residues processed: 93 average time/residue: 1.1902 time to fit residues: 116.8245 Evaluate side-chains 97 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.0040 chunk 53 optimal weight: 0.0980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 252 GLN B 7 ASN B 243 HIS C 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6630 Z= 0.197 Angle : 0.518 13.855 8994 Z= 0.257 Chirality : 0.042 0.164 1034 Planarity : 0.004 0.056 1127 Dihedral : 9.691 85.831 939 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.86 % Allowed : 13.86 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 814 helix: 1.59 (0.25), residues: 452 sheet: -0.72 (0.52), residues: 74 loop : -0.46 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.005 0.001 HIS A 10 PHE 0.010 0.001 PHE C 50 TYR 0.008 0.001 TYR C 251 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.761 Fit side-chains REVERT: A 62 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 180 GLU cc_start: 0.7826 (tt0) cc_final: 0.7451 (tt0) REVERT: A 184 ASP cc_start: 0.8129 (m-30) cc_final: 0.7844 (m-30) REVERT: A 264 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: B 6 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7032 (pp20) REVERT: C 87 MET cc_start: 0.4606 (ptp) cc_final: 0.4115 (pp-130) REVERT: C 208 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.6039 (t80) REVERT: C 231 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6894 (tm-30) outliers start: 13 outliers final: 6 residues processed: 93 average time/residue: 1.1780 time to fit residues: 115.5752 Evaluate side-chains 97 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 252 GLN B 7 ASN B 243 HIS C 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6630 Z= 0.213 Angle : 0.531 13.553 8994 Z= 0.264 Chirality : 0.042 0.169 1034 Planarity : 0.004 0.056 1127 Dihedral : 9.709 87.233 939 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.86 % Allowed : 14.29 % Favored : 83.86 % 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: 0.97 (0.29), residues: 814 helix: 1.60 (0.25), residues: 452 sheet: -0.70 (0.52), residues: 74 loop : -0.44 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.005 0.001 HIS A 10 PHE 0.012 0.001 PHE C 50 TYR 0.008 0.001 TYR C 251 ARG 0.004 0.000 ARG B 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.774 Fit side-chains REVERT: A 62 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7718 (mm) REVERT: A 180 GLU cc_start: 0.7816 (tt0) cc_final: 0.7422 (tt0) REVERT: A 184 ASP cc_start: 0.8130 (m-30) cc_final: 0.7839 (m-30) REVERT: A 264 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: B 6 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7074 (pp20) REVERT: C 87 MET cc_start: 0.4596 (ptp) cc_final: 0.4108 (pp-130) REVERT: C 208 PHE cc_start: 0.6477 (OUTLIER) cc_final: 0.6026 (t80) REVERT: C 231 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6902 (tm-30) outliers start: 13 outliers final: 6 residues processed: 91 average time/residue: 1.2246 time to fit residues: 117.4993 Evaluate side-chains 96 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 0.0370 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 252 GLN B 243 HIS C 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122735 restraints weight = 6332.712| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.54 r_work: 0.3225 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6630 Z= 0.233 Angle : 0.536 13.445 8994 Z= 0.266 Chirality : 0.042 0.162 1034 Planarity : 0.005 0.057 1127 Dihedral : 9.774 87.451 939 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.14 % Allowed : 13.71 % Favored : 84.14 % 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 (0.29), residues: 814 helix: 1.56 (0.25), residues: 454 sheet: -0.70 (0.52), residues: 74 loop : -0.49 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 80 HIS 0.006 0.001 HIS A 10 PHE 0.011 0.001 PHE C 50 TYR 0.009 0.001 TYR B 162 ARG 0.004 0.000 ARG B 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.50 seconds wall clock time: 54 minutes 21.01 seconds (3261.01 seconds total)