Starting phenix.real_space_refine on Wed Sep 17 04:16:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jc2_3245/09_2025/3jc2_3245.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jc2_3245/09_2025/3jc2_3245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jc2_3245/09_2025/3jc2_3245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jc2_3245/09_2025/3jc2_3245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jc2_3245/09_2025/3jc2_3245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jc2_3245/09_2025/3jc2_3245.map" } resolution = 3.6 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= 0.001 sd= 0.019 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 23 5.16 5 C 2569 2.51 5 N 643 2.21 5 O 676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3911 Number of models: 1 Model: "" Number of chains: 4 Chain: "1" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3115 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 3 Chain: "2" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "w" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 142 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "3" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 160 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'UNK:plan-1': 32} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 1.28, per 1000 atoms: 0.33 Number of scatterers: 3911 At special positions: 0 Unit cell: (93.8, 80.4, 84.42, 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 23 16.00 O 676 8.00 N 643 7.00 C 2569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.32 Conformation dependent library (CDL) restraints added in 118.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 74.3% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain '1' and resid 27 through 46 removed outlier: 3.544A pdb=" N THR 1 35 " --> pdb=" O LYS 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 81 through 97 Processing helix chain '1' and resid 105 through 111 Processing helix chain '1' and resid 112 through 134 removed outlier: 3.569A pdb=" N LYS 1 117 " --> pdb=" O ASN 1 113 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR 1 124 " --> pdb=" O GLY 1 120 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE 1 125 " --> pdb=" O MET 1 121 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL 1 132 " --> pdb=" O SER 1 128 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR 1 134 " --> pdb=" O VAL 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 148 through 173 removed outlier: 3.552A pdb=" N VAL 1 162 " --> pdb=" O ALA 1 158 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU 1 169 " --> pdb=" O LEU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 177 through 196 removed outlier: 3.860A pdb=" N PHE 1 182 " --> pdb=" O GLY 1 178 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE 1 183 " --> pdb=" O ILE 1 179 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN 1 186 " --> pdb=" O PHE 1 182 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS 1 188 " --> pdb=" O ALA 1 184 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU 1 189 " --> pdb=" O THR 1 185 " (cutoff:3.500A) Processing helix chain '1' and resid 217 through 223 removed outlier: 3.547A pdb=" N THR 1 222 " --> pdb=" O HIS 1 218 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 259 removed outlier: 3.646A pdb=" N ILE 1 246 " --> pdb=" O LEU 1 242 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA 1 247 " --> pdb=" O MET 1 243 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR 1 257 " --> pdb=" O ALA 1 253 " (cutoff:3.500A) Processing helix chain '1' and resid 285 through 288 Processing helix chain '1' and resid 289 through 312 removed outlier: 3.612A pdb=" N SER 1 299 " --> pdb=" O SER 1 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR 1 302 " --> pdb=" O VAL 1 298 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE 1 304 " --> pdb=" O ASN 1 300 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN 1 306 " --> pdb=" O TYR 1 302 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET 1 307 " --> pdb=" O VAL 1 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA 1 310 " --> pdb=" O GLN 1 306 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG 1 311 " --> pdb=" O MET 1 307 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 1 312 " --> pdb=" O LEU 1 308 " (cutoff:3.500A) Processing helix chain '1' and resid 339 through 345 removed outlier: 3.800A pdb=" N TYR 1 344 " --> pdb=" O GLY 1 340 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU 1 345 " --> pdb=" O LEU 1 341 " (cutoff:3.500A) Processing helix chain '1' and resid 357 through 383 removed outlier: 4.046A pdb=" N ALA 1 361 " --> pdb=" O ASP 1 357 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR 1 364 " --> pdb=" O HIS 1 360 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE 1 365 " --> pdb=" O ALA 1 361 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL 1 366 " --> pdb=" O VAL 1 362 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE 1 367 " --> pdb=" O VAL 1 363 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU 1 381 " --> pdb=" O LYS 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 398 removed outlier: 3.545A pdb=" N VAL 1 390 " --> pdb=" O SER 1 386 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS 1 392 " --> pdb=" O LYS 1 388 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN 1 397 " --> pdb=" O GLN 1 393 " (cutoff:3.500A) Processing helix chain '1' and resid 405 through 415 removed outlier: 3.745A pdb=" N MET 1 409 " --> pdb=" O ARG 1 405 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL 1 410 " --> pdb=" O GLU 1 406 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS 1 411 " --> pdb=" O THR 1 407 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG 1 415 " --> pdb=" O HIS 1 411 " (cutoff:3.500A) Processing helix chain '1' and resid 416 through 439 removed outlier: 3.671A pdb=" N GLY 1 425 " --> pdb=" O ALA 1 421 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA 1 430 " --> pdb=" O LEU 1 426 " (cutoff:3.500A) Processing helix chain '1' and resid 447 through 466 Processing helix chain '2' and resid 8 through 25 removed outlier: 3.511A pdb=" N ARG 2 12 " --> pdb=" O VAL 2 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN 2 13 " --> pdb=" O GLU 2 9 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS 2 16 " --> pdb=" O ARG 2 12 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG 2 20 " --> pdb=" O LYS 2 16 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU 2 21 " --> pdb=" O ASP 2 17 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL 2 22 " --> pdb=" O SER 2 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS 2 23 " --> pdb=" O ILE 2 19 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 57 removed outlier: 3.743A pdb=" N ALA 2 41 " --> pdb=" O ALA 2 37 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE 2 42 " --> pdb=" O MET 2 38 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY 2 43 " --> pdb=" O ALA 2 39 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE 2 44 " --> pdb=" O THR 2 40 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA 2 45 " --> pdb=" O ALA 2 41 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE 2 46 " --> pdb=" O ILE 2 42 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY 2 48 " --> pdb=" O PHE 2 44 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N PHE 2 49 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE 2 50 " --> pdb=" O ILE 2 46 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU 2 56 " --> pdb=" O PHE 2 52 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE 2 57 " --> pdb=" O PHE 2 53 " (cutoff:3.500A) Processing helix chain '2' and resid 58 through 63 removed outlier: 3.899A pdb=" N ASN 2 62 " --> pdb=" O HIS 2 58 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN 2 63 " --> pdb=" O ILE 2 59 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 58 through 63' Processing helix chain 'w' and resid 13 through 28 removed outlier: 3.760A pdb=" N LEU w 24 " --> pdb=" O SER w 20 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS w 25 " --> pdb=" O ASN w 21 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN w 26 " --> pdb=" O LEU w 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY w 27 " --> pdb=" O LEU w 23 " (cutoff:3.500A) Processing helix chain '3' and resid 29 through 48 removed outlier: 3.897A pdb=" N UNK 3 34 " --> pdb=" O UNK 3 30 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK 3 39 " --> pdb=" O UNK 3 35 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N UNK 3 40 " --> pdb=" O UNK 3 36 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N UNK 3 45 " --> pdb=" O UNK 3 41 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N UNK 3 47 " --> pdb=" O UNK 3 43 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N UNK 3 48 " --> pdb=" O UNK 3 44 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain '1' and resid 18 through 19 removed outlier: 6.460A pdb=" N GLU 1 18 " --> pdb=" O UNK 3 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=A Processing sheet with id=B, first strand: chain '1' and resid 262 through 268 207 hydrogen bonds defined for protein. 618 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: 0.54 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 659 1.33 - 1.45: 990 1.45 - 1.57: 2294 1.57 - 1.69: 4 1.69 - 1.82: 36 Bond restraints: 3983 Sorted by residual: bond pdb=" C ILE 1 267 " pdb=" N LYS 1 268 " ideal model delta sigma weight residual 1.330 1.662 -0.331 1.42e-02 4.96e+03 5.44e+02 bond pdb=" C LEU 1 265 " pdb=" N PRO 1 266 " ideal model delta sigma weight residual 1.332 1.388 -0.056 1.30e-02 5.92e+03 1.89e+01 bond pdb=" N PRO 1 266 " pdb=" CD PRO 1 266 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" N ALA 1 215 " pdb=" CA ALA 1 215 " ideal model delta sigma weight residual 1.454 1.500 -0.046 1.27e-02 6.20e+03 1.28e+01 bond pdb=" CA ILE 1 214 " pdb=" C ILE 1 214 " ideal model delta sigma weight residual 1.523 1.567 -0.044 1.27e-02 6.20e+03 1.20e+01 ... (remaining 3978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.72: 5349 5.72 - 11.44: 35 11.44 - 17.16: 5 17.16 - 22.87: 2 22.87 - 28.59: 1 Bond angle restraints: 5392 Sorted by residual: angle pdb=" O ILE 1 267 " pdb=" C ILE 1 267 " pdb=" N LYS 1 268 " ideal model delta sigma weight residual 122.30 93.71 28.59 1.00e+00 1.00e+00 8.18e+02 angle pdb=" O LYS 1 282 " pdb=" C LYS 1 282 " pdb=" N LEU 1 283 " ideal model delta sigma weight residual 123.19 143.48 -20.29 1.17e+00 7.31e-01 3.01e+02 angle pdb=" CA LYS 1 282 " pdb=" C LYS 1 282 " pdb=" N LEU 1 283 " ideal model delta sigma weight residual 115.96 94.92 21.04 1.29e+00 6.01e-01 2.66e+02 angle pdb=" CA ILE 1 267 " pdb=" C ILE 1 267 " pdb=" N LYS 1 268 " ideal model delta sigma weight residual 116.53 128.86 -12.33 9.80e-01 1.04e+00 1.58e+02 angle pdb=" C LYS 1 282 " pdb=" N LEU 1 283 " pdb=" CA LEU 1 283 " ideal model delta sigma weight residual 120.82 104.76 16.06 1.50e+00 4.44e-01 1.15e+02 ... (remaining 5387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 2063 15.48 - 30.96: 220 30.96 - 46.44: 61 46.44 - 61.91: 16 61.91 - 77.39: 5 Dihedral angle restraints: 2365 sinusoidal: 894 harmonic: 1471 Sorted by residual: dihedral pdb=" CA GLY 1 176 " pdb=" C GLY 1 176 " pdb=" N SER 1 177 " pdb=" CA SER 1 177 " ideal model delta harmonic sigma weight residual -180.00 -146.16 -33.84 0 5.00e+00 4.00e-02 4.58e+01 dihedral pdb=" CA PRO 1 198 " pdb=" C PRO 1 198 " pdb=" N THR 1 199 " pdb=" CA THR 1 199 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA THR 1 286 " pdb=" C THR 1 286 " pdb=" N SER 1 287 " pdb=" CA SER 1 287 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 2362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 506 0.083 - 0.166: 110 0.166 - 0.249: 26 0.249 - 0.332: 8 0.332 - 0.414: 2 Chirality restraints: 652 Sorted by residual: chirality pdb=" CA PRO 1 240 " pdb=" N PRO 1 240 " pdb=" C PRO 1 240 " pdb=" CB PRO 1 240 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CA ARG 2 30 " pdb=" N ARG 2 30 " pdb=" C ARG 2 30 " pdb=" CB ARG 2 30 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA GLN 1 397 " pdb=" N GLN 1 397 " pdb=" C GLN 1 397 " pdb=" CB GLN 1 397 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 649 not shown) Planarity restraints: 665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE 1 267 " 0.096 2.00e-02 2.50e+03 1.45e-01 2.10e+02 pdb=" C ILE 1 267 " -0.250 2.00e-02 2.50e+03 pdb=" O ILE 1 267 " 0.086 2.00e-02 2.50e+03 pdb=" N LYS 1 268 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU 1 239 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO 1 240 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO 1 240 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO 1 240 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL 1 433 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C VAL 1 433 " 0.077 2.00e-02 2.50e+03 pdb=" O VAL 1 433 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU 1 434 " -0.026 2.00e-02 2.50e+03 ... (remaining 662 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 2 1.92 - 2.67: 57 2.67 - 3.41: 5691 3.41 - 4.16: 8243 4.16 - 4.90: 14832 Nonbonded interactions: 28825 Sorted by model distance: nonbonded pdb=" O ASN 1 241 " pdb=" OD1 ASN 1 244 " model vdw 1.175 3.040 nonbonded pdb=" N GLY 1 74 " pdb=" OE2 GLU 1 78 " model vdw 1.750 3.120 nonbonded pdb=" O ASN 1 241 " pdb=" CG ASN 1 244 " model vdw 1.976 3.270 nonbonded pdb=" OD1 ASN 1 244 " pdb=" N LEU 1 245 " model vdw 2.224 3.120 nonbonded pdb=" CD LYS 1 268 " pdb=" O SER 1 269 " model vdw 2.259 3.440 ... (remaining 28820 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 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 0.331 3983 Z= 0.847 Angle : 1.630 28.592 5392 Z= 1.092 Chirality : 0.082 0.414 652 Planarity : 0.010 0.145 665 Dihedral : 14.897 77.391 1415 Min Nonbonded Distance : 1.175 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 4.04 % Allowed : 11.49 % Favored : 84.47 % Rotamer: Outliers : 7.32 % Allowed : 9.51 % Favored : 83.17 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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 aren not related in a simple way. whole: -4.52 (0.32), residues: 470 helix: -2.61 (0.25), residues: 266 sheet: -1.35 (1.31), residues: 12 loop : -3.59 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG 1 205 TYR 0.021 0.003 TYR 1 344 PHE 0.039 0.003 PHE 1 351 TRP 0.012 0.002 TRP 1 379 HIS 0.009 0.002 HIS 1 218 Details of bonding type rmsd covalent geometry : bond 0.01225 ( 3983) covalent geometry : angle 1.63030 ( 5392) hydrogen bonds : bond 0.24387 ( 207) hydrogen bonds : angle 9.71590 ( 618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.170 Fit side-chains REVERT: 1 28 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.5689 (t80) REVERT: 1 45 CYS cc_start: 0.6049 (m) cc_final: 0.5006 (t) REVERT: 1 118 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5172 (tt) REVERT: 1 226 LYS cc_start: 0.3341 (OUTLIER) cc_final: 0.2782 (ptmt) REVERT: 1 272 TYR cc_start: 0.8188 (m-80) cc_final: 0.7852 (m-80) REVERT: 1 302 TYR cc_start: 0.2151 (t80) cc_final: 0.1595 (t80) REVERT: 1 377 LYS cc_start: 0.7052 (mtpm) cc_final: 0.5729 (tmtt) REVERT: 1 396 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7334 (tp30) REVERT: 1 400 VAL cc_start: 0.8026 (t) cc_final: 0.7731 (t) REVERT: 1 405 ARG cc_start: 0.5828 (OUTLIER) cc_final: 0.2563 (ptp90) REVERT: 1 457 TYR cc_start: 0.6652 (m-80) cc_final: 0.6408 (t80) REVERT: 2 16 LYS cc_start: 0.8575 (tttt) cc_final: 0.8327 (tttm) REVERT: 2 20 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7449 (tpt170) REVERT: 2 34 GLN cc_start: 0.6074 (tp40) cc_final: 0.5834 (pp30) REVERT: 2 36 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7827 (pt) REVERT: 2 38 MET cc_start: 0.6035 (ttp) cc_final: 0.5815 (ptp) REVERT: 2 47 MET cc_start: 0.5075 (OUTLIER) cc_final: 0.4806 (mmt) outliers start: 30 outliers final: 7 residues processed: 134 average time/residue: 0.0775 time to fit residues: 12.7173 Evaluate side-chains 80 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 PHE Chi-restraints excluded: chain 1 residue 118 LEU Chi-restraints excluded: chain 1 residue 226 LYS Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 240 PRO Chi-restraints excluded: chain 1 residue 255 VAL Chi-restraints excluded: chain 1 residue 346 SER Chi-restraints excluded: chain 1 residue 382 VAL Chi-restraints excluded: chain 1 residue 405 ARG Chi-restraints excluded: chain 1 residue 413 LEU Chi-restraints excluded: chain 1 residue 418 PRO Chi-restraints excluded: chain 2 residue 36 ILE Chi-restraints excluded: chain 2 residue 47 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.0270 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 GLN 1 393 GLN ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.242290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.234858 restraints weight = 8147.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.232420 restraints weight = 9386.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 82)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.231572 restraints weight = 8936.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.230827 restraints weight = 9634.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.230616 restraints weight = 9455.494| |-----------------------------------------------------------------------------| r_work (final): 0.4708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4979 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 3983 Z= 0.183 Angle : 0.821 9.381 5392 Z= 0.411 Chirality : 0.046 0.183 652 Planarity : 0.006 0.095 665 Dihedral : 7.152 50.563 571 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.66 % Favored : 91.49 % Rotamer: Outliers : 6.10 % Allowed : 15.37 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.74 (0.35), residues: 470 helix: -1.19 (0.26), residues: 293 sheet: -0.86 (1.43), residues: 12 loop : -2.91 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 271 TYR 0.014 0.002 TYR 1 276 PHE 0.018 0.002 PHE 1 252 TRP 0.015 0.002 TRP 1 379 HIS 0.007 0.001 HIS 1 218 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3983) covalent geometry : angle 0.82123 ( 5392) hydrogen bonds : bond 0.04380 ( 207) hydrogen bonds : angle 5.14464 ( 618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: 1 118 LEU cc_start: 0.4426 (OUTLIER) cc_final: 0.3314 (mm) REVERT: 1 121 MET cc_start: 0.3860 (tmm) cc_final: 0.3489 (tmm) REVERT: 1 250 PHE cc_start: 0.7713 (t80) cc_final: 0.7174 (t80) REVERT: 1 302 TYR cc_start: 0.1112 (t80) cc_final: 0.0905 (t80) REVERT: 1 357 ASP cc_start: 0.2946 (OUTLIER) cc_final: 0.1476 (p0) outliers start: 25 outliers final: 11 residues processed: 101 average time/residue: 0.0474 time to fit residues: 6.6075 Evaluate side-chains 71 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 118 LEU Chi-restraints excluded: chain 1 residue 163 LEU Chi-restraints excluded: chain 1 residue 179 ILE Chi-restraints excluded: chain 1 residue 188 CYS Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 259 GLN Chi-restraints excluded: chain 1 residue 285 TYR Chi-restraints excluded: chain 1 residue 291 ILE Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 427 CYS Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 186 ASN 1 404 HIS 1 414 ASN ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.235170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.228476 restraints weight = 7821.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.228465 restraints weight = 9523.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 92)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.227733 restraints weight = 8823.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.227667 restraints weight = 8267.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.227277 restraints weight = 8420.745| |-----------------------------------------------------------------------------| r_work (final): 0.4678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 3983 Z= 0.225 Angle : 0.865 12.076 5392 Z= 0.433 Chirality : 0.048 0.246 652 Planarity : 0.006 0.088 665 Dihedral : 6.692 47.107 545 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.72 % Favored : 90.43 % Rotamer: Outliers : 6.59 % Allowed : 19.51 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.24 (0.35), residues: 470 helix: -0.68 (0.27), residues: 290 sheet: -0.13 (1.61), residues: 12 loop : -2.98 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 20 TYR 0.017 0.002 TYR 1 276 PHE 0.023 0.003 PHE 2 33 TRP 0.021 0.003 TRP 1 379 HIS 0.003 0.001 HIS 1 360 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 3983) covalent geometry : angle 0.86454 ( 5392) hydrogen bonds : bond 0.04428 ( 207) hydrogen bonds : angle 5.10891 ( 618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: 1 77 MET cc_start: 0.2369 (mtp) cc_final: 0.2120 (mtm) REVERT: 1 118 LEU cc_start: 0.4114 (OUTLIER) cc_final: 0.2894 (mt) REVERT: 1 226 LYS cc_start: 0.0686 (OUTLIER) cc_final: 0.0081 (ptpt) REVERT: 1 268 LYS cc_start: 0.3547 (tttm) cc_final: 0.2266 (tttm) REVERT: 1 357 ASP cc_start: 0.3119 (OUTLIER) cc_final: 0.1623 (p0) REVERT: 2 20 ARG cc_start: 0.5805 (tpt170) cc_final: 0.4458 (mtt90) outliers start: 27 outliers final: 18 residues processed: 89 average time/residue: 0.0651 time to fit residues: 7.1863 Evaluate side-chains 76 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 118 LEU Chi-restraints excluded: chain 1 residue 163 LEU Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 179 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 1 residue 185 THR Chi-restraints excluded: chain 1 residue 188 CYS Chi-restraints excluded: chain 1 residue 199 THR Chi-restraints excluded: chain 1 residue 219 LEU Chi-restraints excluded: chain 1 residue 226 LYS Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 285 TYR Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 372 CYS Chi-restraints excluded: chain 1 residue 374 PHE Chi-restraints excluded: chain 1 residue 400 VAL Chi-restraints excluded: chain 1 residue 427 CYS Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 7 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.235282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.226737 restraints weight = 7810.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.225288 restraints weight = 8895.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.223821 restraints weight = 10406.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.223611 restraints weight = 9866.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.223344 restraints weight = 8335.172| |-----------------------------------------------------------------------------| r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5315 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3983 Z= 0.163 Angle : 0.757 8.819 5392 Z= 0.373 Chirality : 0.044 0.220 652 Planarity : 0.005 0.082 665 Dihedral : 6.384 50.529 545 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.85 % Allowed : 6.81 % Favored : 92.34 % Rotamer: Outliers : 7.32 % Allowed : 19.76 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.85 (0.36), residues: 470 helix: -0.45 (0.27), residues: 299 sheet: 0.14 (1.78), residues: 12 loop : -2.76 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 20 TYR 0.015 0.002 TYR 1 344 PHE 0.012 0.002 PHE 1 252 TRP 0.022 0.002 TRP 1 379 HIS 0.004 0.001 HIS 2 58 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3983) covalent geometry : angle 0.75684 ( 5392) hydrogen bonds : bond 0.03855 ( 207) hydrogen bonds : angle 4.66032 ( 618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.145 Fit side-chains REVERT: 1 77 MET cc_start: 0.1840 (mtp) cc_final: 0.1573 (mtm) REVERT: 1 118 LEU cc_start: 0.4039 (OUTLIER) cc_final: 0.2816 (mt) REVERT: 1 268 LYS cc_start: 0.3796 (tttm) cc_final: 0.2504 (tttm) REVERT: 1 357 ASP cc_start: 0.2933 (OUTLIER) cc_final: 0.1678 (p0) REVERT: 1 434 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5268 (mt) REVERT: 2 20 ARG cc_start: 0.5714 (tpt170) cc_final: 0.4342 (mtt90) outliers start: 30 outliers final: 18 residues processed: 85 average time/residue: 0.0497 time to fit residues: 5.7008 Evaluate side-chains 79 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 118 LEU Chi-restraints excluded: chain 1 residue 163 LEU Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 1 residue 185 THR Chi-restraints excluded: chain 1 residue 188 CYS Chi-restraints excluded: chain 1 residue 207 MET Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 285 TYR Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 374 PHE Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 400 VAL Chi-restraints excluded: chain 1 residue 427 CYS Chi-restraints excluded: chain 1 residue 434 LEU Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 32 GLU Chi-restraints excluded: chain 2 residue 50 ILE Chi-restraints excluded: chain w residue 24 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 17 optimal weight: 0.0770 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 overall best weight: 3.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.233554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.225342 restraints weight = 7808.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.223818 restraints weight = 9709.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.222875 restraints weight = 9057.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.221920 restraints weight = 9818.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.221652 restraints weight = 11574.301| |-----------------------------------------------------------------------------| r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.7172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 3983 Z= 0.167 Angle : 0.769 9.145 5392 Z= 0.377 Chirality : 0.045 0.224 652 Planarity : 0.005 0.077 665 Dihedral : 6.265 53.824 545 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.87 % Favored : 91.28 % Rotamer: Outliers : 6.34 % Allowed : 21.95 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.36), residues: 470 helix: -0.41 (0.27), residues: 301 sheet: -0.33 (1.74), residues: 12 loop : -2.81 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG w 12 TYR 0.013 0.002 TYR 1 173 PHE 0.017 0.002 PHE 1 252 TRP 0.028 0.004 TRP 1 379 HIS 0.003 0.001 HIS 1 360 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 3983) covalent geometry : angle 0.76853 ( 5392) hydrogen bonds : bond 0.03798 ( 207) hydrogen bonds : angle 4.54757 ( 618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.146 Fit side-chains REVERT: 1 226 LYS cc_start: 0.2352 (OUTLIER) cc_final: 0.1353 (ptpt) REVERT: 1 268 LYS cc_start: 0.4213 (tttm) cc_final: 0.3234 (tttm) REVERT: 1 357 ASP cc_start: 0.3304 (OUTLIER) cc_final: 0.2248 (p0) REVERT: 2 20 ARG cc_start: 0.5486 (tpt170) cc_final: 0.4183 (mtt90) outliers start: 26 outliers final: 20 residues processed: 75 average time/residue: 0.0605 time to fit residues: 5.8613 Evaluate side-chains 73 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 163 LEU Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 179 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 1 residue 185 THR Chi-restraints excluded: chain 1 residue 188 CYS Chi-restraints excluded: chain 1 residue 207 MET Chi-restraints excluded: chain 1 residue 226 LYS Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 285 TYR Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 374 PHE Chi-restraints excluded: chain 1 residue 400 VAL Chi-restraints excluded: chain 1 residue 407 THR Chi-restraints excluded: chain 1 residue 427 CYS Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 24 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 40.0000 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.236066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.231140 restraints weight = 8557.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.230718 restraints weight = 9173.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.230266 restraints weight = 9428.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.230107 restraints weight = 9192.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.230083 restraints weight = 8148.687| |-----------------------------------------------------------------------------| r_work (final): 0.4686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5256 moved from start: 0.7661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3983 Z= 0.155 Angle : 0.724 8.043 5392 Z= 0.361 Chirality : 0.044 0.183 652 Planarity : 0.005 0.075 665 Dihedral : 6.077 56.080 543 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.66 % Favored : 91.49 % Rotamer: Outliers : 6.34 % Allowed : 23.41 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.36), residues: 470 helix: -0.35 (0.27), residues: 303 sheet: -0.33 (1.67), residues: 12 loop : -2.85 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG w 12 TYR 0.012 0.002 TYR 1 276 PHE 0.017 0.002 PHE 1 252 TRP 0.032 0.004 TRP 1 379 HIS 0.003 0.001 HIS 1 218 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3983) covalent geometry : angle 0.72439 ( 5392) hydrogen bonds : bond 0.03631 ( 207) hydrogen bonds : angle 4.45839 ( 618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.152 Fit side-chains REVERT: 1 268 LYS cc_start: 0.4464 (tttm) cc_final: 0.3101 (tttp) REVERT: 1 356 GLU cc_start: 0.3303 (OUTLIER) cc_final: 0.1739 (pp20) REVERT: 1 357 ASP cc_start: 0.3219 (OUTLIER) cc_final: 0.2255 (p0) REVERT: 2 20 ARG cc_start: 0.5478 (tpt170) cc_final: 0.3955 (mtt90) outliers start: 26 outliers final: 19 residues processed: 71 average time/residue: 0.0664 time to fit residues: 5.9599 Evaluate side-chains 71 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 163 LEU Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 179 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 1 residue 185 THR Chi-restraints excluded: chain 1 residue 188 CYS Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 285 TYR Chi-restraints excluded: chain 1 residue 356 GLU Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 374 PHE Chi-restraints excluded: chain 1 residue 400 VAL Chi-restraints excluded: chain 1 residue 407 THR Chi-restraints excluded: chain 1 residue 427 CYS Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.234605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.227156 restraints weight = 8137.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.225102 restraints weight = 10387.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.224533 restraints weight = 10284.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.224131 restraints weight = 10750.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 83)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.223669 restraints weight = 9598.202| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 0.7893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3983 Z= 0.133 Angle : 0.704 11.946 5392 Z= 0.347 Chirality : 0.043 0.196 652 Planarity : 0.005 0.069 665 Dihedral : 5.921 58.116 543 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.87 % Favored : 91.28 % Rotamer: Outliers : 5.12 % Allowed : 24.39 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.69 (0.36), residues: 470 helix: -0.33 (0.27), residues: 306 sheet: -0.50 (1.62), residues: 12 loop : -2.73 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG w 12 TYR 0.012 0.002 TYR 1 276 PHE 0.016 0.001 PHE 1 196 TRP 0.042 0.004 TRP 1 379 HIS 0.002 0.001 HIS 1 411 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3983) covalent geometry : angle 0.70424 ( 5392) hydrogen bonds : bond 0.03462 ( 207) hydrogen bonds : angle 4.31572 ( 618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.135 Fit side-chains REVERT: 1 44 VAL cc_start: 0.7917 (m) cc_final: 0.7634 (t) REVERT: 1 133 MET cc_start: 0.5480 (ppp) cc_final: 0.4840 (ppp) REVERT: 1 207 MET cc_start: 0.3037 (OUTLIER) cc_final: 0.1692 (mmm) REVERT: 1 268 LYS cc_start: 0.4510 (tttm) cc_final: 0.3001 (tmmt) REVERT: 1 356 GLU cc_start: 0.3184 (OUTLIER) cc_final: 0.1740 (pp20) REVERT: 1 357 ASP cc_start: 0.3092 (OUTLIER) cc_final: 0.2264 (p0) REVERT: 2 20 ARG cc_start: 0.5403 (tpt170) cc_final: 0.3957 (mtt90) outliers start: 21 outliers final: 16 residues processed: 69 average time/residue: 0.0563 time to fit residues: 5.0718 Evaluate side-chains 72 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 163 LEU Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 179 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 1 residue 185 THR Chi-restraints excluded: chain 1 residue 188 CYS Chi-restraints excluded: chain 1 residue 207 MET Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 356 GLU Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 374 PHE Chi-restraints excluded: chain 1 residue 400 VAL Chi-restraints excluded: chain 1 residue 407 THR Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Chi-restraints excluded: chain w residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 127 GLN ** 1 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.230834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.226295 restraints weight = 8281.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.225808 restraints weight = 11366.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.225470 restraints weight = 10914.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.225295 restraints weight = 9938.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.225120 restraints weight = 9725.405| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5394 moved from start: 0.8381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 3983 Z= 0.205 Angle : 0.819 10.346 5392 Z= 0.409 Chirality : 0.047 0.193 652 Planarity : 0.006 0.072 665 Dihedral : 6.639 55.547 543 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 1.06 % Allowed : 8.09 % Favored : 90.85 % Rotamer: Outliers : 5.85 % Allowed : 24.63 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.99 (0.36), residues: 470 helix: -0.52 (0.27), residues: 301 sheet: -0.35 (1.72), residues: 12 loop : -2.90 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 1 24 TYR 0.018 0.002 TYR 1 173 PHE 0.016 0.002 PHE 1 252 TRP 0.051 0.005 TRP 1 379 HIS 0.005 0.002 HIS 1 360 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 3983) covalent geometry : angle 0.81863 ( 5392) hydrogen bonds : bond 0.04321 ( 207) hydrogen bonds : angle 4.75824 ( 618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.145 Fit side-chains REVERT: 1 44 VAL cc_start: 0.7887 (m) cc_final: 0.7685 (t) REVERT: 1 133 MET cc_start: 0.5848 (ppp) cc_final: 0.4849 (ppp) REVERT: 1 182 PHE cc_start: 0.5033 (m-80) cc_final: 0.4639 (m-80) REVERT: 1 207 MET cc_start: 0.3238 (OUTLIER) cc_final: 0.1739 (mmm) REVERT: 1 356 GLU cc_start: 0.3330 (OUTLIER) cc_final: 0.1843 (pp20) REVERT: 1 357 ASP cc_start: 0.3601 (OUTLIER) cc_final: 0.2208 (p0) REVERT: 2 20 ARG cc_start: 0.5635 (tpt170) cc_final: 0.4038 (mtt90) REVERT: 2 33 PHE cc_start: 0.5344 (OUTLIER) cc_final: 0.4631 (m-80) outliers start: 24 outliers final: 16 residues processed: 69 average time/residue: 0.0556 time to fit residues: 5.1014 Evaluate side-chains 70 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 122 ILE Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 179 ILE Chi-restraints excluded: chain 1 residue 185 THR Chi-restraints excluded: chain 1 residue 188 CYS Chi-restraints excluded: chain 1 residue 207 MET Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 285 TYR Chi-restraints excluded: chain 1 residue 356 GLU Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 374 PHE Chi-restraints excluded: chain 1 residue 407 THR Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 33 PHE Chi-restraints excluded: chain 2 residue 50 ILE Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 1 optimal weight: 0.0060 chunk 35 optimal weight: 3.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.232519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.228018 restraints weight = 8314.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.227609 restraints weight = 11536.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.226942 restraints weight = 10831.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.226464 restraints weight = 12450.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 75)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.226247 restraints weight = 12046.074| |-----------------------------------------------------------------------------| r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.8561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3983 Z= 0.165 Angle : 0.740 10.311 5392 Z= 0.369 Chirality : 0.045 0.192 652 Planarity : 0.005 0.070 665 Dihedral : 6.386 58.697 543 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.30 % Favored : 90.85 % Rotamer: Outliers : 4.39 % Allowed : 26.83 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.95 (0.35), residues: 470 helix: -0.44 (0.27), residues: 302 sheet: -0.42 (1.65), residues: 12 loop : -3.00 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG w 12 TYR 0.013 0.002 TYR 1 276 PHE 0.016 0.002 PHE 1 196 TRP 0.062 0.005 TRP 1 379 HIS 0.003 0.001 HIS 1 411 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3983) covalent geometry : angle 0.74016 ( 5392) hydrogen bonds : bond 0.03891 ( 207) hydrogen bonds : angle 4.57817 ( 618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.147 Fit side-chains REVERT: 1 44 VAL cc_start: 0.7983 (m) cc_final: 0.7775 (t) REVERT: 1 133 MET cc_start: 0.5848 (ppp) cc_final: 0.5084 (ppp) REVERT: 1 182 PHE cc_start: 0.5222 (m-80) cc_final: 0.4849 (m-80) REVERT: 1 207 MET cc_start: 0.3067 (OUTLIER) cc_final: 0.1650 (mmm) REVERT: 1 268 LYS cc_start: 0.4601 (tttm) cc_final: 0.3298 (tttp) REVERT: 1 356 GLU cc_start: 0.3184 (OUTLIER) cc_final: 0.1778 (pp20) REVERT: 1 357 ASP cc_start: 0.3261 (OUTLIER) cc_final: 0.2169 (p0) REVERT: 2 20 ARG cc_start: 0.5551 (tpt170) cc_final: 0.3994 (mtt90) REVERT: w 12 ARG cc_start: 0.5000 (mtm180) cc_final: 0.4794 (mtm180) outliers start: 18 outliers final: 14 residues processed: 67 average time/residue: 0.0604 time to fit residues: 5.3010 Evaluate side-chains 70 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 179 ILE Chi-restraints excluded: chain 1 residue 185 THR Chi-restraints excluded: chain 1 residue 188 CYS Chi-restraints excluded: chain 1 residue 207 MET Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 356 GLU Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 374 PHE Chi-restraints excluded: chain 1 residue 407 THR Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.233285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.228704 restraints weight = 8291.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.228163 restraints weight = 12139.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.227678 restraints weight = 11030.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.227146 restraints weight = 12079.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.226867 restraints weight = 12567.953| |-----------------------------------------------------------------------------| r_work (final): 0.4646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.8732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 3983 Z= 0.151 Angle : 0.723 10.068 5392 Z= 0.360 Chirality : 0.044 0.185 652 Planarity : 0.005 0.067 665 Dihedral : 6.269 58.997 543 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.66 % Favored : 91.49 % Rotamer: Outliers : 4.63 % Allowed : 27.32 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.35), residues: 470 helix: -0.39 (0.27), residues: 303 sheet: -0.32 (1.71), residues: 12 loop : -3.07 (0.43), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 20 TYR 0.012 0.002 TYR 1 276 PHE 0.015 0.001 PHE 1 196 TRP 0.067 0.006 TRP 1 379 HIS 0.002 0.001 HIS 1 411 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3983) covalent geometry : angle 0.72251 ( 5392) hydrogen bonds : bond 0.03749 ( 207) hydrogen bonds : angle 4.55609 ( 618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.148 Fit side-chains REVERT: 1 44 VAL cc_start: 0.7927 (m) cc_final: 0.7616 (t) REVERT: 1 133 MET cc_start: 0.6004 (ppp) cc_final: 0.5372 (ppp) REVERT: 1 182 PHE cc_start: 0.5216 (m-80) cc_final: 0.4824 (m-80) REVERT: 1 207 MET cc_start: 0.2967 (OUTLIER) cc_final: 0.1505 (mmm) REVERT: 1 239 LEU cc_start: 0.2923 (OUTLIER) cc_final: 0.2456 (pp) REVERT: 1 268 LYS cc_start: 0.4544 (tttm) cc_final: 0.3225 (tttp) REVERT: 1 356 GLU cc_start: 0.3186 (OUTLIER) cc_final: 0.1776 (pp20) REVERT: 1 357 ASP cc_start: 0.3124 (OUTLIER) cc_final: 0.2153 (p0) REVERT: 2 20 ARG cc_start: 0.5515 (tpt170) cc_final: 0.3975 (mtt90) REVERT: w 12 ARG cc_start: 0.4982 (mtm180) cc_final: 0.4633 (mtm180) outliers start: 19 outliers final: 13 residues processed: 69 average time/residue: 0.0604 time to fit residues: 5.4234 Evaluate side-chains 72 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 179 ILE Chi-restraints excluded: chain 1 residue 185 THR Chi-restraints excluded: chain 1 residue 188 CYS Chi-restraints excluded: chain 1 residue 207 MET Chi-restraints excluded: chain 1 residue 239 LEU Chi-restraints excluded: chain 1 residue 356 GLU Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 374 PHE Chi-restraints excluded: chain 1 residue 407 THR Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 47 optimal weight: 40.0000 chunk 46 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.231946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.227546 restraints weight = 8331.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.227032 restraints weight = 11861.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.226460 restraints weight = 10715.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.226033 restraints weight = 10499.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.226005 restraints weight = 10476.205| |-----------------------------------------------------------------------------| r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.8926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3983 Z= 0.165 Angle : 0.741 9.917 5392 Z= 0.369 Chirality : 0.045 0.197 652 Planarity : 0.005 0.066 665 Dihedral : 6.339 59.707 543 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.09 % Favored : 91.06 % Rotamer: Outliers : 4.39 % Allowed : 27.56 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.35), residues: 470 helix: -0.38 (0.27), residues: 302 sheet: -0.26 (1.74), residues: 12 loop : -3.15 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 1 271 TYR 0.013 0.002 TYR 1 276 PHE 0.016 0.002 PHE 1 196 TRP 0.064 0.005 TRP 1 379 HIS 0.002 0.001 HIS 1 360 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3983) covalent geometry : angle 0.74054 ( 5392) hydrogen bonds : bond 0.03891 ( 207) hydrogen bonds : angle 4.62897 ( 618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 856.11 seconds wall clock time: 15 minutes 28.72 seconds (928.72 seconds total)