Starting phenix.real_space_refine on Tue Sep 24 07:16:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp1_37707/09_2024/8wp1_37707_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp1_37707/09_2024/8wp1_37707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp1_37707/09_2024/8wp1_37707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp1_37707/09_2024/8wp1_37707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp1_37707/09_2024/8wp1_37707_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp1_37707/09_2024/8wp1_37707_trim.cif" } resolution = 3.15 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= -0.002 sd= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4685 2.51 5 N 1232 2.21 5 O 1357 1.98 5 H 2 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7328 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2481 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain: "C" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1834 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2568 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {'U9S': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.13, per 1000 atoms: 0.70 Number of scatterers: 7328 At special positions: 0 Unit cell: (69.7, 103.7, 140.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1357 8.00 N 1232 7.00 C 4685 6.00 H 2 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 11 " - pdb=" SG CYS A 268 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.0 seconds 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 44.3% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 24 through 50 Processing helix chain 'A' and resid 56 through 75 removed outlier: 3.787A pdb=" N THR A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 82 removed outlier: 4.030A pdb=" N SER A 82 " --> pdb=" O MET A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 121 removed outlier: 3.849A pdb=" N ILE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 135 through 155 removed outlier: 3.686A pdb=" N ILE A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.636A pdb=" N ASN A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.847A pdb=" N SER A 178 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 196 through 219 Processing helix chain 'A' and resid 228 through 259 removed outlier: 3.600A pdb=" N VAL A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.675A pdb=" N ASN A 253 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 Proline residue: A 282 - end of helix removed outlier: 3.967A pdb=" N PHE A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 297 removed outlier: 4.135A pdb=" N VAL A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.833A pdb=" N TRP C 211 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 273 through 279 removed outlier: 4.491A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.809A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 4 through 24 removed outlier: 3.774A pdb=" N GLU D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 removed outlier: 4.406A pdb=" N ASN D 36 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 23 removed outlier: 3.897A pdb=" N LYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.369A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.779A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.944A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET D 61 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 71 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.823A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.704A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.807A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.536A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.762A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1026 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: 2.04 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2 1.03 - 1.23: 34 1.23 - 1.42: 3122 1.42 - 1.62: 4245 1.62 - 1.81: 74 Bond restraints: 7477 Sorted by residual: bond pdb=" C THR D 274 " pdb=" O THR D 274 " ideal model delta sigma weight residual 1.236 1.137 0.099 1.39e-02 5.18e+03 5.05e+01 bond pdb=" C VAL D 315 " pdb=" O VAL D 315 " ideal model delta sigma weight residual 1.237 1.156 0.081 1.19e-02 7.06e+03 4.66e+01 bond pdb=" C ASN C 255 " pdb=" O ASN C 255 " ideal model delta sigma weight residual 1.235 1.158 0.077 1.33e-02 5.65e+03 3.35e+01 bond pdb=" N THR D 274 " pdb=" CA THR D 274 " ideal model delta sigma weight residual 1.455 1.395 0.060 1.33e-02 5.65e+03 2.03e+01 bond pdb=" C GLU E 58 " pdb=" O GLU E 58 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.31e-02 5.83e+03 1.96e+01 ... (remaining 7472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 9894 1.67 - 3.33: 186 3.33 - 5.00: 37 5.00 - 6.67: 6 6.67 - 8.33: 5 Bond angle restraints: 10128 Sorted by residual: angle pdb=" N ASN C 255 " pdb=" CA ASN C 255 " pdb=" CB ASN C 255 " ideal model delta sigma weight residual 110.47 102.14 8.33 1.45e+00 4.76e-01 3.30e+01 angle pdb=" O SER E 57 " pdb=" C SER E 57 " pdb=" N GLU E 58 " ideal model delta sigma weight residual 121.87 127.56 -5.69 1.05e+00 9.07e-01 2.94e+01 angle pdb=" CA SER E 57 " pdb=" C SER E 57 " pdb=" N GLU E 58 " ideal model delta sigma weight residual 118.87 113.02 5.85 1.18e+00 7.18e-01 2.46e+01 angle pdb=" CA THR D 274 " pdb=" C THR D 274 " pdb=" N SER D 275 " ideal model delta sigma weight residual 118.40 124.47 -6.07 1.28e+00 6.10e-01 2.25e+01 angle pdb=" C VAL D 315 " pdb=" CA VAL D 315 " pdb=" CB VAL D 315 " ideal model delta sigma weight residual 111.32 116.98 -5.66 1.21e+00 6.83e-01 2.19e+01 ... (remaining 10123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3832 17.59 - 35.18: 476 35.18 - 52.77: 117 52.77 - 70.36: 19 70.36 - 87.95: 10 Dihedral angle restraints: 4454 sinusoidal: 1753 harmonic: 2701 Sorted by residual: dihedral pdb=" CB CYS A 95 " pdb=" SG CYS A 95 " pdb=" SG CYS A 172 " pdb=" CB CYS A 172 " ideal model delta sinusoidal sigma weight residual -86.00 -166.83 80.83 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS A 11 " pdb=" SG CYS A 11 " pdb=" SG CYS A 268 " pdb=" CB CYS A 268 " ideal model delta sinusoidal sigma weight residual -86.00 -126.03 40.03 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" N ASN C 255 " pdb=" C ASN C 255 " pdb=" CA ASN C 255 " pdb=" CB ASN C 255 " ideal model delta harmonic sigma weight residual 122.80 111.97 10.83 0 2.50e+00 1.60e-01 1.88e+01 ... (remaining 4451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 906 0.046 - 0.092: 200 0.092 - 0.138: 48 0.138 - 0.184: 1 0.184 - 0.230: 4 Chirality restraints: 1159 Sorted by residual: chirality pdb=" C04 U9S A 401 " pdb=" C02 U9S A 401 " pdb=" C05 U9S A 401 " pdb=" O09 U9S A 401 " both_signs ideal model delta sigma weight residual True 2.16 2.39 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB THR D 274 " pdb=" CA THR D 274 " pdb=" OG1 THR D 274 " pdb=" CG2 THR D 274 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA VAL D 315 " pdb=" N VAL D 315 " pdb=" C VAL D 315 " pdb=" CB VAL D 315 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1156 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 76 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 77 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 235 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO D 236 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 255 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C ASN C 255 " -0.027 2.00e-02 2.50e+03 pdb=" O ASN C 255 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN C 256 " 0.009 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 8 2.28 - 2.86: 2756 2.86 - 3.44: 7907 3.44 - 4.02: 13075 4.02 - 4.60: 20367 Nonbonded interactions: 44113 Sorted by model distance: nonbonded pdb=" OH TYR A 277 " pdb=" H1 HOH A 601 " model vdw 1.698 2.450 nonbonded pdb=" O08 U9S A 401 " pdb=" H2 HOH A 601 " model vdw 1.889 2.450 nonbonded pdb=" OE1 GLN C 52 " pdb=" ND2 ASN C 331 " model vdw 2.208 2.950 nonbonded pdb=" OE2 GLU A 18 " pdb=" ND2 ASN A 274 " model vdw 2.229 2.950 nonbonded pdb=" OD1 ASN D 16 " pdb=" NH2 ARG D 19 " model vdw 2.231 2.950 ... (remaining 44108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.190 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.500 Find NCS groups from input model: 0.080 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 : 0.004 0.099 7475 Z= 0.273 Angle : 0.589 8.334 10127 Z= 0.350 Chirality : 0.041 0.230 1159 Planarity : 0.003 0.058 1278 Dihedral : 16.530 87.954 2698 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.37 % Allowed : 18.16 % Favored : 81.47 % Cbeta Deviations : 0.11 % 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: 0.33 (0.30), residues: 909 helix: 1.99 (0.29), residues: 386 sheet: -0.70 (0.38), residues: 165 loop : -1.32 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 82 HIS 0.003 0.001 HIS D 142 PHE 0.011 0.001 PHE A 115 TYR 0.020 0.001 TYR A 46 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.902 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.2600 time to fit residues: 32.0472 Evaluate side-chains 92 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7475 Z= 0.251 Angle : 0.493 5.532 10127 Z= 0.271 Chirality : 0.041 0.152 1159 Planarity : 0.004 0.052 1278 Dihedral : 4.562 31.101 1003 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.99 % Allowed : 18.03 % Favored : 78.98 % 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: 0.54 (0.30), residues: 909 helix: 2.20 (0.28), residues: 379 sheet: -0.52 (0.37), residues: 178 loop : -1.25 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 332 HIS 0.006 0.001 HIS C 188 PHE 0.013 0.002 PHE A 115 TYR 0.019 0.001 TYR A 46 ARG 0.003 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.826 Fit side-chains REVERT: A 298 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7938 (mp) outliers start: 24 outliers final: 16 residues processed: 102 average time/residue: 0.2403 time to fit residues: 31.8492 Evaluate side-chains 107 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7475 Z= 0.226 Angle : 0.468 5.180 10127 Z= 0.257 Chirality : 0.040 0.142 1159 Planarity : 0.004 0.053 1278 Dihedral : 4.473 31.798 1001 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.99 % Allowed : 20.77 % Favored : 76.24 % 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: 0.61 (0.30), residues: 909 helix: 2.31 (0.28), residues: 378 sheet: -0.56 (0.37), residues: 178 loop : -1.21 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 82 HIS 0.005 0.001 HIS C 188 PHE 0.012 0.001 PHE C 196 TYR 0.020 0.001 TYR A 46 ARG 0.002 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.841 Fit side-chains REVERT: A 190 CYS cc_start: 0.8378 (m) cc_final: 0.8090 (m) REVERT: A 298 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7907 (mp) REVERT: C 276 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8281 (pp20) outliers start: 24 outliers final: 17 residues processed: 101 average time/residue: 0.2457 time to fit residues: 31.8186 Evaluate side-chains 108 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7475 Z= 0.223 Angle : 0.465 5.164 10127 Z= 0.254 Chirality : 0.040 0.135 1159 Planarity : 0.003 0.052 1278 Dihedral : 4.446 31.685 1001 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.86 % Allowed : 20.52 % Favored : 75.62 % 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: 0.65 (0.30), residues: 909 helix: 2.38 (0.28), residues: 378 sheet: -0.54 (0.37), residues: 178 loop : -1.25 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.004 0.001 HIS D 142 PHE 0.012 0.001 PHE C 196 TYR 0.020 0.001 TYR A 46 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 0.992 Fit side-chains REVERT: A 152 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7674 (mp) REVERT: A 190 CYS cc_start: 0.8373 (m) cc_final: 0.8087 (m) REVERT: A 298 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7929 (mp) REVERT: C 276 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8297 (pp20) outliers start: 31 outliers final: 22 residues processed: 109 average time/residue: 0.2361 time to fit residues: 33.4519 Evaluate side-chains 116 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.0010 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 0.0020 chunk 17 optimal weight: 3.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7475 Z= 0.218 Angle : 0.460 5.088 10127 Z= 0.252 Chirality : 0.040 0.137 1159 Planarity : 0.003 0.052 1278 Dihedral : 4.411 31.564 1001 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.98 % Allowed : 20.77 % Favored : 75.25 % 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: 0.73 (0.30), residues: 909 helix: 2.45 (0.28), residues: 378 sheet: -0.50 (0.37), residues: 175 loop : -1.21 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.004 0.001 HIS D 142 PHE 0.012 0.001 PHE C 196 TYR 0.020 0.001 TYR A 46 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 0.746 Fit side-chains REVERT: A 152 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7685 (mp) REVERT: A 190 CYS cc_start: 0.8365 (m) cc_final: 0.8090 (m) REVERT: A 298 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7924 (mp) REVERT: C 276 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8274 (pp20) outliers start: 32 outliers final: 26 residues processed: 108 average time/residue: 0.2283 time to fit residues: 31.9816 Evaluate side-chains 118 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7475 Z= 0.188 Angle : 0.440 4.743 10127 Z= 0.242 Chirality : 0.040 0.135 1159 Planarity : 0.003 0.050 1278 Dihedral : 4.315 31.681 1001 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.98 % Allowed : 20.77 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.30), residues: 909 helix: 2.53 (0.28), residues: 380 sheet: -0.54 (0.37), residues: 178 loop : -1.16 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.004 0.001 HIS C 188 PHE 0.013 0.001 PHE A 34 TYR 0.019 0.001 TYR A 46 ARG 0.001 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 0.887 Fit side-chains REVERT: A 190 CYS cc_start: 0.8350 (m) cc_final: 0.8078 (m) REVERT: A 255 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6715 (ttt90) REVERT: A 298 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7935 (mp) REVERT: C 276 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8282 (pp20) outliers start: 32 outliers final: 26 residues processed: 111 average time/residue: 0.2472 time to fit residues: 35.4297 Evaluate side-chains 120 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7475 Z= 0.299 Angle : 0.509 6.334 10127 Z= 0.276 Chirality : 0.042 0.157 1159 Planarity : 0.004 0.057 1278 Dihedral : 4.558 32.751 1001 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.35 % Allowed : 20.77 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 909 helix: 2.35 (0.28), residues: 380 sheet: -0.60 (0.37), residues: 178 loop : -1.24 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.005 0.001 HIS D 142 PHE 0.014 0.002 PHE A 112 TYR 0.020 0.001 TYR A 46 ARG 0.002 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 91 time to evaluate : 0.790 Fit side-chains REVERT: A 190 CYS cc_start: 0.8382 (m) cc_final: 0.8117 (m) REVERT: A 255 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6908 (ttt90) REVERT: A 298 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7997 (mp) REVERT: C 46 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7420 (mtpp) REVERT: C 276 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8245 (pp20) outliers start: 35 outliers final: 26 residues processed: 111 average time/residue: 0.2445 time to fit residues: 34.7016 Evaluate side-chains 119 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 0.0370 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7475 Z= 0.299 Angle : 0.508 6.318 10127 Z= 0.276 Chirality : 0.041 0.151 1159 Planarity : 0.004 0.058 1278 Dihedral : 4.608 33.608 1001 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.23 % Allowed : 20.65 % Favored : 75.12 % 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: 0.59 (0.29), residues: 909 helix: 2.26 (0.28), residues: 383 sheet: -0.53 (0.37), residues: 176 loop : -1.27 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 82 HIS 0.005 0.001 HIS C 188 PHE 0.014 0.002 PHE C 196 TYR 0.020 0.001 TYR A 46 ARG 0.002 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 0.906 Fit side-chains REVERT: A 190 CYS cc_start: 0.8415 (m) cc_final: 0.8161 (m) REVERT: A 255 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6876 (ttt90) REVERT: C 46 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7406 (mtpp) REVERT: C 276 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8260 (pp20) outliers start: 34 outliers final: 28 residues processed: 109 average time/residue: 0.2545 time to fit residues: 35.3211 Evaluate side-chains 119 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7475 Z= 0.170 Angle : 0.435 4.799 10127 Z= 0.240 Chirality : 0.039 0.135 1159 Planarity : 0.003 0.053 1278 Dihedral : 4.311 33.821 1001 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.73 % Allowed : 21.14 % Favored : 75.12 % 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: 0.87 (0.30), residues: 909 helix: 2.56 (0.28), residues: 382 sheet: -0.46 (0.38), residues: 175 loop : -1.14 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 82 HIS 0.004 0.001 HIS C 188 PHE 0.010 0.001 PHE C 196 TYR 0.018 0.001 TYR A 46 ARG 0.001 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 0.820 Fit side-chains REVERT: A 190 CYS cc_start: 0.8344 (m) cc_final: 0.8067 (m) REVERT: A 255 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6673 (ttt90) REVERT: A 298 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7962 (mp) REVERT: C 46 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7390 (mtpp) REVERT: C 276 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8281 (pp20) outliers start: 30 outliers final: 26 residues processed: 107 average time/residue: 0.2521 time to fit residues: 34.4802 Evaluate side-chains 119 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 0.0870 chunk 89 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7475 Z= 0.217 Angle : 0.459 5.034 10127 Z= 0.252 Chirality : 0.040 0.136 1159 Planarity : 0.003 0.054 1278 Dihedral : 4.366 34.238 1001 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.73 % Allowed : 21.27 % 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: 0.82 (0.30), residues: 909 helix: 2.54 (0.28), residues: 382 sheet: -0.51 (0.37), residues: 178 loop : -1.17 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.005 0.001 HIS C 188 PHE 0.014 0.001 PHE A 34 TYR 0.019 0.001 TYR A 46 ARG 0.001 0.000 ARG A 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.839 Fit side-chains REVERT: A 190 CYS cc_start: 0.8355 (m) cc_final: 0.8086 (m) REVERT: A 255 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6725 (ttt90) REVERT: A 298 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7971 (mp) REVERT: C 46 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7413 (mtpp) REVERT: C 276 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8288 (pp20) outliers start: 30 outliers final: 26 residues processed: 106 average time/residue: 0.2525 time to fit residues: 34.2403 Evaluate side-chains 118 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101002 restraints weight = 8209.649| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.38 r_work: 0.2841 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7475 Z= 0.177 Angle : 0.433 4.814 10127 Z= 0.239 Chirality : 0.039 0.134 1159 Planarity : 0.003 0.053 1278 Dihedral : 4.246 34.030 1001 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.73 % Allowed : 21.27 % 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: 0.92 (0.30), residues: 909 helix: 2.64 (0.28), residues: 383 sheet: -0.47 (0.38), residues: 178 loop : -1.17 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 82 HIS 0.004 0.001 HIS C 188 PHE 0.010 0.001 PHE C 196 TYR 0.018 0.001 TYR A 46 ARG 0.001 0.000 ARG A 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.45 seconds wall clock time: 35 minutes 0.07 seconds (2100.07 seconds total)