Starting phenix.real_space_refine on Fri Oct 23 01:19:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r10_53489/10_2026/9r10_53489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r10_53489/10_2026/9r10_53489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r10_53489/10_2026/9r10_53489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r10_53489/10_2026/9r10_53489.map" model { file = "/net/cci-nas-00/data/ceres_data/9r10_53489/10_2026/9r10_53489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r10_53489/10_2026/9r10_53489.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4825 2.51 5 N 1175 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7335 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3730 Classifications: {'peptide': 486} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 475} Chain breaks: 1 Chain: "H" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1707 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 215} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1628 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 241 Unusual residues: {'CLR': 8, 'SD9': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.64, per 1000 atoms: 0.22 Number of scatterers: 7335 At special positions: 0 Unit cell: (77.35, 72.8, 143.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1302 8.00 N 1175 7.00 C 4825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.98 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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: 0.62 Conformation dependent library (CDL) restraints added in 293.0 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 51.8% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 27 through 62 removed outlier: 3.515A pdb=" N LEU A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Proline residue: A 44 - end of helix removed outlier: 3.790A pdb=" N ILE A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 68 through 85 removed outlier: 3.819A pdb=" N ASP A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 3.529A pdb=" N SER A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 126 through 136 removed outlier: 3.724A pdb=" N ASN A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.914A pdb=" N ARG A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 180 removed outlier: 4.485A pdb=" N ALA A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 207 Processing helix chain 'A' and resid 212 through 239 Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.954A pdb=" N CYS A 252 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 288 removed outlier: 4.070A pdb=" N PHE A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 3.885A pdb=" N GLU A 273 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 326 removed outlier: 4.756A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 328 through 356 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.901A pdb=" N ILE A 364 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 403 Proline residue: A 380 - end of helix removed outlier: 4.099A pdb=" N LEU A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.798A pdb=" N GLY A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 430 removed outlier: 3.684A pdb=" N ILE A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 460 removed outlier: 3.709A pdb=" N LEU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.852A pdb=" N ALA A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 567 removed outlier: 3.770A pdb=" N LEU A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 88 removed outlier: 4.085A pdb=" N THR H 88 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 107 removed outlier: 3.637A pdb=" N PHE H 106 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 203 removed outlier: 3.958A pdb=" N GLN H 203 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.730A pdb=" N SER L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.663A pdb=" N TYR H 91 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 17 through 21 Processing sheet with id=AA3, first strand: chain 'H' and resid 17 through 21 Processing sheet with id=AA4, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.671A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.671A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.551A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR H 205 " --> pdb=" O VAL H 222 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.630A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.747A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER L 176 " --> pdb=" O SER L 162 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 145 through 148 removed outlier: 3.638A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1224 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: 0.91 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.28: 1094 1.28 - 1.42: 1968 1.42 - 1.57: 4413 1.57 - 1.71: 0 1.71 - 1.86: 46 Bond restraints: 7521 Sorted by residual: bond pdb=" C10 SD9 A 608 " pdb=" N5 SD9 A 608 " ideal model delta sigma weight residual 1.303 1.452 -0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C8 SD9 A 608 " pdb=" N5 SD9 A 608 " ideal model delta sigma weight residual 1.326 1.459 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" C8 SD9 A 608 " pdb=" N3 SD9 A 608 " ideal model delta sigma weight residual 1.349 1.457 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C8 SD9 A 608 " pdb=" N4 SD9 A 608 " ideal model delta sigma weight residual 1.334 1.246 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C2 SD9 A 608 " pdb=" N2 SD9 A 608 " ideal model delta sigma weight residual 1.367 1.305 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 7516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 10172 2.63 - 5.27: 106 5.27 - 7.90: 10 7.90 - 10.53: 2 10.53 - 13.16: 1 Bond angle restraints: 10291 Sorted by residual: angle pdb=" C CYS L 88 " pdb=" CA CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sigma weight residual 110.24 101.91 8.33 1.88e+00 2.83e-01 1.96e+01 angle pdb=" C SER L 31 " pdb=" CA SER L 31 " pdb=" CB SER L 31 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 angle pdb=" CA LEU A 558 " pdb=" CB LEU A 558 " pdb=" CG LEU A 558 " ideal model delta sigma weight residual 116.30 129.46 -13.16 3.50e+00 8.16e-02 1.41e+01 angle pdb=" N THR A 367 " pdb=" CA THR A 367 " pdb=" C THR A 367 " ideal model delta sigma weight residual 114.56 109.93 4.63 1.27e+00 6.20e-01 1.33e+01 angle pdb=" C ASN A 136 " pdb=" CA ASN A 136 " pdb=" CB ASN A 136 " ideal model delta sigma weight residual 111.50 115.84 -4.34 1.29e+00 6.01e-01 1.13e+01 ... (remaining 10286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.10: 4425 24.10 - 48.20: 345 48.20 - 72.30: 42 72.30 - 96.39: 10 96.39 - 120.49: 3 Dihedral angle restraints: 4825 sinusoidal: 2160 harmonic: 2665 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 93 " pdb=" CB CYS H 93 " ideal model delta sinusoidal sigma weight residual 93.00 171.41 -78.41 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 146.88 -53.88 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -35.46 -50.54 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 4822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1096 0.063 - 0.125: 131 0.125 - 0.188: 5 0.188 - 0.250: 0 0.250 - 0.313: 1 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CA CYS L 88 " pdb=" N CYS L 88 " pdb=" C CYS L 88 " pdb=" CB CYS L 88 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C17 CLR A 601 " pdb=" C13 CLR A 601 " pdb=" C16 CLR A 601 " pdb=" C20 CLR A 601 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" C20 CLR A 604 " pdb=" C17 CLR A 604 " pdb=" C21 CLR A 604 " pdb=" C22 CLR A 604 " both_signs ideal model delta sigma weight residual False 2.59 2.42 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 1230 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 567 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C VAL A 567 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL A 567 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG A 568 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 128 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO A 129 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 195 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO H 196 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 196 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 196 " 0.026 5.00e-02 4.00e+02 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 615 2.74 - 3.28: 7177 3.28 - 3.82: 11849 3.82 - 4.36: 13823 4.36 - 4.90: 25076 Nonbonded interactions: 58540 Sorted by model distance: nonbonded pdb=" OD2 ASP A 72 " pdb=" CE2 TYR H 55 " model vdw 2.198 3.340 nonbonded pdb=" OH TYR A 177 " pdb=" OG1 THR A 244 " model vdw 2.207 3.040 nonbonded pdb=" ND1 HIS H 211 " pdb=" OG SER H 214 " model vdw 2.252 3.120 nonbonded pdb=" O SER L 30 " pdb=" OG SER L 30 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU A 34 " pdb=" NE2 GLN A 331 " model vdw 2.282 3.120 ... (remaining 58535 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: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.012 0.948 7525 Z= 0.597 Angle : 0.778 30.942 10299 Z= 0.411 Chirality : 0.041 0.313 1233 Planarity : 0.004 0.049 1218 Dihedral : 16.151 120.493 3107 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 5.15 % Allowed : 21.65 % Favored : 73.20 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.29), residues: 916 helix: 1.93 (0.25), residues: 432 sheet: -1.71 (0.38), residues: 189 loop : -2.02 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 211 TYR 0.014 0.002 TYR H 60 PHE 0.010 0.001 PHE A 62 TRP 0.010 0.001 TRP A 439 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.24 ( 7521) covalent geometry : angle 0.68546 / 0.37 (10291) SS BOND : bond 0.47388 / 24.94 ( 4) SS BOND : angle 13.24422 / 7.59 ( 8) hydrogen bonds : bond 0.17471 / 11.87 ( 412) hydrogen bonds : angle 7.23022 / 5.11 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9178 (mp) REVERT: A 179 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8823 (tt) outliers start: 40 outliers final: 26 residues processed: 155 average time/residue: 0.0906 time to fit residues: 18.6500 Evaluate side-chains 115 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN H 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.084161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.066834 restraints weight = 16989.931| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.21 r_work: 0.2700 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7525 Z= 0.152 Angle : 0.598 7.613 10299 Z= 0.306 Chirality : 0.040 0.172 1233 Planarity : 0.005 0.041 1218 Dihedral : 8.529 84.726 1624 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 5.67 % Allowed : 22.55 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.30), residues: 916 helix: 2.37 (0.25), residues: 440 sheet: -1.26 (0.40), residues: 181 loop : -1.87 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.015 0.001 TYR H 80 PHE 0.011 0.001 PHE A 456 TRP 0.013 0.001 TRP A 439 HIS 0.001 0.000 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7521) covalent geometry : angle 0.59668 / 0.31 (10291) SS BOND : bond 0.00292 / 0.15 ( 4) SS BOND : angle 1.58626 / 1.05 ( 8) hydrogen bonds : bond 0.04607 / 3.14 ( 412) hydrogen bonds : angle 5.18353 / 3.67 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8542 (mm-30) REVERT: A 70 GLU cc_start: 0.8316 (mp0) cc_final: 0.7997 (mp0) REVERT: A 179 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8898 (tt) REVERT: H 73 ASP cc_start: 0.7536 (t0) cc_final: 0.7281 (t70) REVERT: L 89 GLN cc_start: 0.9228 (tt0) cc_final: 0.9026 (tt0) REVERT: L 122 ASP cc_start: 0.8687 (p0) cc_final: 0.8455 (p0) REVERT: L 142 ARG cc_start: 0.8534 (tpt-90) cc_final: 0.8268 (tpt-90) REVERT: L 167 ASP cc_start: 0.8009 (t0) cc_final: 0.7790 (t0) outliers start: 44 outliers final: 24 residues processed: 138 average time/residue: 0.0826 time to fit residues: 15.5079 Evaluate side-chains 116 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [34, 25, 65, 69, 17, 80, 87, 43, 39, 23, 41] chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 HIS A 187 GLN A 449 GLN L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.083773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.066440 restraints weight = 17062.347| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.46 r_work: 0.2692 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7525 Z= 0.135 Angle : 0.566 7.817 10299 Z= 0.289 Chirality : 0.039 0.172 1233 Planarity : 0.004 0.041 1218 Dihedral : 7.261 81.564 1596 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 5.54 % Allowed : 22.29 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.30), residues: 916 helix: 2.41 (0.25), residues: 447 sheet: -0.95 (0.40), residues: 180 loop : -1.58 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 84 TYR 0.009 0.001 TYR L 173 PHE 0.012 0.001 PHE A 456 TRP 0.012 0.001 TRP A 439 HIS 0.002 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7521) covalent geometry : angle 0.56536 / 0.29 (10291) SS BOND : bond 0.00358 / 0.18 ( 4) SS BOND : angle 1.02092 / 0.67 ( 8) hydrogen bonds : bond 0.04249 / 2.88 ( 412) hydrogen bonds : angle 4.72359 / 3.36 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8594 (mm-30) REVERT: A 70 GLU cc_start: 0.8360 (mp0) cc_final: 0.7982 (mp0) REVERT: A 72 ASP cc_start: 0.9049 (m-30) cc_final: 0.8835 (m-30) REVERT: A 368 ASP cc_start: 0.8683 (t0) cc_final: 0.8406 (t0) REVERT: H 73 ASP cc_start: 0.7640 (t0) cc_final: 0.7415 (t0) REVERT: H 86 GLU cc_start: 0.9172 (pt0) cc_final: 0.8854 (tm-30) REVERT: H 203 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6053 (pm20) REVERT: H 204 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.6811 (t) REVERT: H 221 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8466 (tmtt) REVERT: L 89 GLN cc_start: 0.9218 (tt0) cc_final: 0.8950 (tt0) REVERT: L 122 ASP cc_start: 0.8842 (p0) cc_final: 0.8550 (p0) REVERT: L 167 ASP cc_start: 0.8176 (t0) cc_final: 0.7639 (t0) outliers start: 43 outliers final: 25 residues processed: 126 average time/residue: 0.0751 time to fit residues: 13.1404 Evaluate side-chains 115 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 203 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [1, 70, 74, 66, 24, 30, 49, 21, 16, 50, 4] chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 0.0370 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 0.0020 overall best weight: 0.4266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.086503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.069046 restraints weight = 17212.334| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.28 r_work: 0.2718 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7525 Z= 0.111 Angle : 0.541 9.237 10299 Z= 0.273 Chirality : 0.039 0.173 1233 Planarity : 0.004 0.042 1218 Dihedral : 6.712 76.649 1591 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.04 % Favored : 95.85 % Rotamer: Outliers : 5.28 % Allowed : 23.20 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.30), residues: 916 helix: 2.54 (0.25), residues: 447 sheet: -0.40 (0.42), residues: 169 loop : -1.63 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.009 0.001 TYR A 382 PHE 0.012 0.001 PHE A 456 TRP 0.014 0.001 TRP A 439 HIS 0.001 0.000 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7521) covalent geometry : angle 0.54081 / 0.27 (10291) SS BOND : bond 0.00287 / 0.14 ( 4) SS BOND : angle 0.81665 / 0.54 ( 8) hydrogen bonds : bond 0.03936 / 2.68 ( 412) hydrogen bonds : angle 4.43415 / 3.14 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8585 (mm-30) REVERT: A 66 LEU cc_start: 0.9268 (mt) cc_final: 0.8969 (mt) REVERT: A 70 GLU cc_start: 0.8334 (mp0) cc_final: 0.7899 (mp0) REVERT: A 72 ASP cc_start: 0.9028 (m-30) cc_final: 0.8796 (m-30) REVERT: A 368 ASP cc_start: 0.8700 (t0) cc_final: 0.8368 (t0) REVERT: H 73 ASP cc_start: 0.7612 (t0) cc_final: 0.7342 (t0) REVERT: H 84 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.7666 (mtm-85) REVERT: H 86 GLU cc_start: 0.9148 (pt0) cc_final: 0.8748 (tm-30) REVERT: H 203 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6141 (pm20) REVERT: H 204 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.7040 (t) REVERT: H 221 LYS cc_start: 0.8725 (tttp) cc_final: 0.8382 (tmtt) REVERT: L 79 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7830 (mt0) REVERT: L 89 GLN cc_start: 0.9139 (tt0) cc_final: 0.8826 (tt0) REVERT: L 122 ASP cc_start: 0.8886 (p0) cc_final: 0.8555 (p0) REVERT: L 167 ASP cc_start: 0.8245 (t0) cc_final: 0.7669 (t0) REVERT: L 187 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8768 (mm-30) outliers start: 41 outliers final: 28 residues processed: 125 average time/residue: 0.0753 time to fit residues: 13.2372 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [50, 66, 53, 77, 73, 80, 22, 16, 41, 8, 26] chunk 50 optimal weight: 4.9990 chunk 66 optimal weight: 0.0020 chunk 53 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN H 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.068619 restraints weight = 17033.807| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.24 r_work: 0.2733 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7525 Z= 0.108 Angle : 0.544 8.908 10299 Z= 0.273 Chirality : 0.038 0.173 1233 Planarity : 0.004 0.048 1218 Dihedral : 6.477 73.054 1591 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 5.15 % Allowed : 22.94 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.30), residues: 916 helix: 2.59 (0.25), residues: 448 sheet: -0.19 (0.42), residues: 169 loop : -1.56 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 24 TYR 0.009 0.001 TYR A 382 PHE 0.012 0.001 PHE A 456 TRP 0.015 0.001 TRP A 439 HIS 0.001 0.000 HIS H 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 7521) covalent geometry : angle 0.54416 / 0.27 (10291) SS BOND : bond 0.00306 / 0.15 ( 4) SS BOND : angle 0.87833 / 0.63 ( 8) hydrogen bonds : bond 0.03798 / 2.59 ( 412) hydrogen bonds : angle 4.34769 / 3.08 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8588 (mm-30) REVERT: A 66 LEU cc_start: 0.9272 (mt) cc_final: 0.8966 (mt) REVERT: A 70 GLU cc_start: 0.8337 (mp0) cc_final: 0.7889 (mp0) REVERT: A 72 ASP cc_start: 0.9038 (m-30) cc_final: 0.8791 (m-30) REVERT: A 278 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8927 (mm-30) REVERT: A 368 ASP cc_start: 0.8743 (t0) cc_final: 0.8335 (t0) REVERT: H 73 ASP cc_start: 0.7611 (t0) cc_final: 0.7354 (t0) REVERT: H 86 GLU cc_start: 0.9162 (pt0) cc_final: 0.8811 (tm-30) REVERT: H 203 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: L 79 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: L 89 GLN cc_start: 0.9116 (tt0) cc_final: 0.8765 (tt0) REVERT: L 122 ASP cc_start: 0.8897 (p0) cc_final: 0.8555 (p0) REVERT: L 158 ASN cc_start: 0.9329 (p0) cc_final: 0.9117 (p0) REVERT: L 167 ASP cc_start: 0.8291 (t0) cc_final: 0.7669 (t0) outliers start: 40 outliers final: 28 residues processed: 128 average time/residue: 0.0775 time to fit residues: 13.8221 Evaluate side-chains 120 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [77, 73, 80, 20, 86, 83, 62, 58, 85, 17, 60] chunk 77 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 ASN H 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.085311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.068217 restraints weight = 16911.475| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.23 r_work: 0.2723 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7525 Z= 0.120 Angle : 0.566 8.370 10299 Z= 0.280 Chirality : 0.038 0.172 1233 Planarity : 0.004 0.047 1218 Dihedral : 6.290 66.796 1591 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.74 % Rotamer: Outliers : 5.28 % Allowed : 23.58 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.30), residues: 916 helix: 2.77 (0.25), residues: 443 sheet: -0.04 (0.42), residues: 169 loop : -1.51 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 24 TYR 0.009 0.001 TYR A 382 PHE 0.012 0.001 PHE A 456 TRP 0.014 0.001 TRP A 439 HIS 0.001 0.000 HIS H 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7521) covalent geometry : angle 0.56519 / 0.28 (10291) SS BOND : bond 0.00328 / 0.16 ( 4) SS BOND : angle 0.89437 / 0.64 ( 8) hydrogen bonds : bond 0.03816 / 2.60 ( 412) hydrogen bonds : angle 4.24655 / 3.00 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8627 (mm-30) REVERT: A 66 LEU cc_start: 0.9284 (mt) cc_final: 0.8975 (mt) REVERT: A 70 GLU cc_start: 0.8388 (mp0) cc_final: 0.7920 (mp0) REVERT: A 278 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8938 (mm-30) REVERT: A 368 ASP cc_start: 0.8775 (t0) cc_final: 0.8306 (t0) REVERT: H 73 ASP cc_start: 0.7657 (t0) cc_final: 0.7350 (t0) REVERT: H 84 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7624 (mtm-85) REVERT: H 86 GLU cc_start: 0.9151 (pt0) cc_final: 0.8756 (tm-30) REVERT: H 203 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: L 79 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: L 89 GLN cc_start: 0.9114 (tt0) cc_final: 0.8743 (tt0) REVERT: L 122 ASP cc_start: 0.8915 (p0) cc_final: 0.8579 (p0) REVERT: L 167 ASP cc_start: 0.8340 (t0) cc_final: 0.7756 (t0) outliers start: 41 outliers final: 31 residues processed: 125 average time/residue: 0.0795 time to fit residues: 13.9196 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [11, 9, 78, 66, 2, 64, 50, 21, 25, 43, 85] chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.083226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.065933 restraints weight = 17383.866| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.24 r_work: 0.2655 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7525 Z= 0.215 Angle : 0.622 9.471 10299 Z= 0.308 Chirality : 0.040 0.168 1233 Planarity : 0.004 0.054 1218 Dihedral : 6.210 66.311 1587 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 4.90 % Allowed : 24.48 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.30), residues: 916 helix: 2.75 (0.25), residues: 441 sheet: 0.07 (0.42), residues: 170 loop : -1.54 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.011 0.001 TYR A 382 PHE 0.013 0.001 PHE L 139 TRP 0.011 0.001 TRP A 439 HIS 0.002 0.001 HIS H 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 ( 7521) covalent geometry : angle 0.62143 / 0.31 (10291) SS BOND : bond 0.00599 / 0.30 ( 4) SS BOND : angle 1.19013 / 0.85 ( 8) hydrogen bonds : bond 0.04518 / 3.06 ( 412) hydrogen bonds : angle 4.41980 / 3.13 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8638 (mm-30) REVERT: A 70 GLU cc_start: 0.8499 (mp0) cc_final: 0.8083 (mp0) REVERT: A 278 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8963 (mm-30) REVERT: A 368 ASP cc_start: 0.8856 (t0) cc_final: 0.8381 (t0) REVERT: H 73 ASP cc_start: 0.7692 (t0) cc_final: 0.7360 (t0) REVERT: H 86 GLU cc_start: 0.9132 (pt0) cc_final: 0.8807 (tm-30) REVERT: H 203 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: L 79 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: L 89 GLN cc_start: 0.9131 (tt0) cc_final: 0.8745 (tt0) REVERT: L 122 ASP cc_start: 0.8960 (p0) cc_final: 0.8633 (p0) REVERT: L 167 ASP cc_start: 0.8426 (t0) cc_final: 0.7760 (t0) REVERT: L 187 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8797 (mm-30) outliers start: 38 outliers final: 30 residues processed: 119 average time/residue: 0.0768 time to fit residues: 12.9399 Evaluate side-chains 116 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [9, 52, 59, 65, 68, 53, 46, 73, 72, 50, 7] chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.083940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.066844 restraints weight = 17376.964| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.27 r_work: 0.2698 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7525 Z= 0.126 Angle : 0.582 11.157 10299 Z= 0.286 Chirality : 0.039 0.172 1233 Planarity : 0.004 0.055 1218 Dihedral : 5.965 61.213 1587 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Rotamer: Outliers : 4.25 % Allowed : 25.00 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.30), residues: 916 helix: 2.81 (0.25), residues: 441 sheet: 0.15 (0.43), residues: 169 loop : -1.44 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 24 TYR 0.010 0.001 TYR L 173 PHE 0.012 0.001 PHE H 133 TRP 0.015 0.001 TRP A 439 HIS 0.001 0.000 HIS H 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7521) covalent geometry : angle 0.58191 / 0.29 (10291) SS BOND : bond 0.00347 / 0.17 ( 4) SS BOND : angle 0.91790 / 0.64 ( 8) hydrogen bonds : bond 0.04023 / 2.74 ( 412) hydrogen bonds : angle 4.24052 / 3.00 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.9335 (mt) cc_final: 0.9014 (mt) REVERT: A 70 GLU cc_start: 0.8442 (mp0) cc_final: 0.7995 (mp0) REVERT: A 278 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8967 (mm-30) REVERT: A 368 ASP cc_start: 0.8823 (t0) cc_final: 0.8342 (t0) REVERT: H 43 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8460 (mmmm) REVERT: H 73 ASP cc_start: 0.7660 (t0) cc_final: 0.7335 (t0) REVERT: H 86 GLU cc_start: 0.9142 (pt0) cc_final: 0.8789 (tm-30) REVERT: H 95 ARG cc_start: 0.8694 (ptt-90) cc_final: 0.8357 (ptt90) REVERT: H 203 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: L 79 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: L 89 GLN cc_start: 0.9110 (tt0) cc_final: 0.8718 (tt0) REVERT: L 122 ASP cc_start: 0.8947 (p0) cc_final: 0.8625 (p0) REVERT: L 167 ASP cc_start: 0.8414 (t0) cc_final: 0.7722 (t0) REVERT: L 187 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8804 (mm-30) outliers start: 33 outliers final: 30 residues processed: 117 average time/residue: 0.0785 time to fit residues: 12.6501 Evaluate side-chains 119 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [46, 14, 33, 4, 24, 87, 89, 71, 19, 73, 72] chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.085657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.068594 restraints weight = 16967.489| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.23 r_work: 0.2730 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7525 Z= 0.111 Angle : 0.576 10.886 10299 Z= 0.283 Chirality : 0.038 0.172 1233 Planarity : 0.004 0.056 1218 Dihedral : 5.606 53.297 1587 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 4.64 % Allowed : 24.87 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.30), residues: 916 helix: 2.92 (0.25), residues: 441 sheet: 0.29 (0.43), residues: 169 loop : -1.36 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 24 TYR 0.009 0.001 TYR A 382 PHE 0.011 0.001 PHE A 456 TRP 0.015 0.001 TRP A 439 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 7521) covalent geometry : angle 0.57554 / 0.28 (10291) SS BOND : bond 0.00290 / 0.14 ( 4) SS BOND : angle 0.79511 / 0.57 ( 8) hydrogen bonds : bond 0.03737 / 2.54 ( 412) hydrogen bonds : angle 4.08642 / 2.89 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.9303 (mt) cc_final: 0.8990 (mt) REVERT: A 70 GLU cc_start: 0.8449 (mp0) cc_final: 0.8009 (mp0) REVERT: A 179 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8812 (tt) REVERT: A 187 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: A 278 GLU cc_start: 0.9280 (mm-30) cc_final: 0.9001 (mm-30) REVERT: A 368 ASP cc_start: 0.8808 (t0) cc_final: 0.8348 (t0) REVERT: H 43 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8453 (mmmm) REVERT: H 73 ASP cc_start: 0.7747 (t0) cc_final: 0.7428 (t0) REVERT: H 84 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.7692 (mtm-85) REVERT: H 86 GLU cc_start: 0.9170 (pt0) cc_final: 0.8765 (tm-30) REVERT: H 95 ARG cc_start: 0.8777 (ptt-90) cc_final: 0.8417 (ptt90) REVERT: H 203 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: L 89 GLN cc_start: 0.9086 (tt0) cc_final: 0.8685 (tt0) REVERT: L 122 ASP cc_start: 0.8929 (p0) cc_final: 0.8602 (p0) REVERT: L 167 ASP cc_start: 0.8434 (t0) cc_final: 0.7764 (t0) outliers start: 36 outliers final: 30 residues processed: 123 average time/residue: 0.0769 time to fit residues: 13.1672 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [3, 58, 77, 65, 14, 26, 59, 54, 21, 48, 52] chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.0010 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.085375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.068338 restraints weight = 16928.839| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.23 r_work: 0.2725 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7525 Z= 0.124 Angle : 0.591 10.846 10299 Z= 0.291 Chirality : 0.039 0.171 1233 Planarity : 0.004 0.062 1218 Dihedral : 5.564 53.330 1587 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 4.64 % Allowed : 25.00 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.30), residues: 916 helix: 2.92 (0.25), residues: 442 sheet: 0.05 (0.42), residues: 179 loop : -1.22 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 24 TYR 0.009 0.001 TYR A 382 PHE 0.012 0.001 PHE H 29 TRP 0.013 0.001 TRP A 439 HIS 0.001 0.000 HIS H 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7521) covalent geometry : angle 0.58979 / 0.29 (10291) SS BOND : bond 0.00371 / 0.19 ( 4) SS BOND : angle 1.24953 / 0.79 ( 8) hydrogen bonds : bond 0.03772 / 2.57 ( 412) hydrogen bonds : angle 4.07675 / 2.89 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.9313 (mt) cc_final: 0.9001 (mt) REVERT: A 70 GLU cc_start: 0.8473 (mp0) cc_final: 0.8023 (mp0) REVERT: A 278 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9007 (mm-30) REVERT: A 368 ASP cc_start: 0.8827 (t0) cc_final: 0.8371 (t0) REVERT: H 43 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8480 (mmmm) REVERT: H 73 ASP cc_start: 0.7834 (t0) cc_final: 0.7513 (t0) REVERT: H 84 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.7713 (mtm-85) REVERT: H 86 GLU cc_start: 0.9168 (pt0) cc_final: 0.8766 (tm-30) REVERT: H 95 ARG cc_start: 0.8804 (ptt-90) cc_final: 0.8539 (ptt90) REVERT: H 203 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: L 89 GLN cc_start: 0.9089 (tt0) cc_final: 0.8679 (tt0) REVERT: L 122 ASP cc_start: 0.8926 (p0) cc_final: 0.8603 (p0) REVERT: L 167 ASP cc_start: 0.8441 (t0) cc_final: 0.7769 (t0) outliers start: 36 outliers final: 32 residues processed: 124 average time/residue: 0.0701 time to fit residues: 12.1706 Evaluate side-chains 120 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [20, 54, 56, 23, 77, 33, 37, 48, 10, 8, 82] chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.068223 restraints weight = 16931.448| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.23 r_work: 0.2721 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7525 Z= 0.126 Angle : 0.584 10.176 10299 Z= 0.288 Chirality : 0.038 0.171 1233 Planarity : 0.004 0.063 1218 Dihedral : 5.506 53.495 1587 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.04 % Favored : 95.85 % Rotamer: Outliers : 4.25 % Allowed : 25.77 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.30), residues: 916 helix: 2.95 (0.25), residues: 441 sheet: 0.14 (0.43), residues: 180 loop : -1.21 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 24 TYR 0.010 0.001 TYR A 382 PHE 0.010 0.001 PHE A 456 TRP 0.012 0.001 TRP A 439 HIS 0.001 0.000 HIS H 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7521) covalent geometry : angle 0.58338 / 0.29 (10291) SS BOND : bond 0.00375 / 0.19 ( 4) SS BOND : angle 1.07169 / 0.72 ( 8) hydrogen bonds : bond 0.03859 / 2.62 ( 412) hydrogen bonds : angle 4.09435 / 2.89 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1727.72 seconds wall clock time: 30 minutes 32.18 seconds (1832.18 seconds total)