Starting phenix.real_space_refine on Wed Mar 5 22:39:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jc2_3245/03_2025/3jc2_3245.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jc2_3245/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3jc2_3245/03_2025/3jc2_3245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jc2_3245/03_2025/3jc2_3245.map" model { file = "/net/cci-nas-00/data/ceres_data/3jc2_3245/03_2025/3jc2_3245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jc2_3245/03_2025/3jc2_3245.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.82, per 1000 atoms: 0.98 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: 0.91 Conformation dependent library (CDL) restraints added in 469.2 milliseconds 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: 0.31 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: 0.84 Time building geometry restraints manager: 1.10 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: 4.500 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.120 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.020 ------------------------------------------------------------------------------- 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= 0.762 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 : 18.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.002 TRP 1 379 HIS 0.009 0.002 HIS 1 218 PHE 0.039 0.003 PHE 1 351 TYR 0.021 0.003 TYR 1 344 ARG 0.022 0.001 ARG 1 205 *********************** 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 : 0.411 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: 0.1702 time to fit residues: 27.5829 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 : 0.337 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.0470 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 overall best weight: 1.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 393 GLN ** 1 456 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 = 0.4837 r_free = 0.4837 target = 0.242691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.235267 restraints weight = 7967.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.232885 restraints weight = 9258.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.232854 restraints weight = 9793.923| |-----------------------------------------------------------------------------| r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4891 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 3983 Z= 0.250 Angle : 0.818 9.080 5392 Z= 0.409 Chirality : 0.046 0.186 652 Planarity : 0.006 0.096 665 Dihedral : 7.159 51.392 571 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.45 % Favored : 91.70 % Rotamer: Outliers : 5.37 % Allowed : 16.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.35), residues: 470 helix: -1.15 (0.26), residues: 293 sheet: -0.89 (1.42), residues: 12 loop : -2.92 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 1 379 HIS 0.007 0.002 HIS 1 218 PHE 0.018 0.002 PHE 1 252 TYR 0.013 0.002 TYR 1 364 ARG 0.007 0.001 ARG 1 205 *********************** 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 106 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: 1 118 LEU cc_start: 0.4605 (OUTLIER) cc_final: 0.3467 (mm) REVERT: 1 121 MET cc_start: 0.4130 (tmm) cc_final: 0.3787 (tmm) REVERT: 1 191 ILE cc_start: 0.4767 (tp) cc_final: 0.4562 (tp) REVERT: 1 250 PHE cc_start: 0.7733 (t80) cc_final: 0.7205 (t80) REVERT: 1 302 TYR cc_start: 0.1026 (t80) cc_final: 0.0819 (t80) REVERT: 1 357 ASP cc_start: 0.2768 (OUTLIER) cc_final: 0.1215 (p0) outliers start: 22 outliers final: 8 residues processed: 100 average time/residue: 0.1286 time to fit residues: 16.9908 Evaluate side-chains 70 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 188 CYS 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 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 45 optimal weight: 7.9990 chunk 18 optimal weight: 0.0050 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 3.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 186 ASN ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.238494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.232117 restraints weight = 7907.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.231320 restraints weight = 10605.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.230758 restraints weight = 9896.786| |-----------------------------------------------------------------------------| r_work (final): 0.4713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5060 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3983 Z= 0.273 Angle : 0.783 10.784 5392 Z= 0.388 Chirality : 0.045 0.213 652 Planarity : 0.006 0.085 665 Dihedral : 6.330 47.261 545 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.30 % Favored : 90.85 % Rotamer: Outliers : 6.34 % Allowed : 20.00 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.36), residues: 470 helix: -0.49 (0.28), residues: 292 sheet: 0.05 (1.65), residues: 12 loop : -2.74 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP 1 379 HIS 0.002 0.001 HIS 1 343 PHE 0.021 0.002 PHE 2 53 TYR 0.015 0.002 TYR 1 276 ARG 0.004 0.001 ARG 2 20 *********************** 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 98 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.439 Fit side-chains REVERT: 1 77 MET cc_start: 0.2361 (mtp) cc_final: 0.2159 (mtm) REVERT: 1 118 LEU cc_start: 0.3931 (OUTLIER) cc_final: 0.2681 (mt) REVERT: 1 191 ILE cc_start: 0.4907 (tp) cc_final: 0.4679 (tp) REVERT: 1 226 LYS cc_start: 0.0677 (OUTLIER) cc_final: 0.0239 (ptpt) REVERT: 1 268 LYS cc_start: 0.4274 (tttm) cc_final: 0.3118 (tttm) REVERT: 1 357 ASP cc_start: 0.3203 (OUTLIER) cc_final: 0.1719 (p0) REVERT: 2 20 ARG cc_start: 0.5506 (tpt170) cc_final: 0.4545 (tpt90) outliers start: 26 outliers final: 16 residues processed: 91 average time/residue: 0.1587 time to fit residues: 18.1072 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 : 0.372 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain 1 residue 226 LYS 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 357 ASP Chi-restraints excluded: chain 1 residue 374 PHE 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 41 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 34 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 27 optimal weight: 0.2980 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.240775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.234277 restraints weight = 7906.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.234237 restraints weight = 10552.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.233766 restraints weight = 9301.932| |-----------------------------------------------------------------------------| r_work (final): 0.4747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4954 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3983 Z= 0.169 Angle : 0.697 8.847 5392 Z= 0.341 Chirality : 0.043 0.247 652 Planarity : 0.005 0.078 665 Dihedral : 5.843 52.848 545 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.85 % Allowed : 6.17 % Favored : 92.98 % Rotamer: Outliers : 6.34 % Allowed : 21.71 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.36), residues: 470 helix: -0.13 (0.28), residues: 294 sheet: 0.45 (1.76), residues: 12 loop : -2.44 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 1 379 HIS 0.001 0.000 HIS 1 411 PHE 0.013 0.001 PHE 1 252 TYR 0.013 0.002 TYR 1 344 ARG 0.007 0.000 ARG w 12 *********************** 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 88 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: 1 123 ILE cc_start: 0.4232 (OUTLIER) cc_final: 0.3974 (pt) REVERT: 1 179 ILE cc_start: 0.5364 (OUTLIER) cc_final: 0.4738 (tp) REVERT: 1 191 ILE cc_start: 0.4930 (tp) cc_final: 0.4684 (tp) REVERT: 1 243 MET cc_start: 0.6488 (tpt) cc_final: 0.4478 (mtt) REVERT: 1 268 LYS cc_start: 0.4490 (tttm) cc_final: 0.3233 (tttp) REVERT: 1 434 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4340 (tp) REVERT: 2 20 ARG cc_start: 0.5337 (tpt170) cc_final: 0.4438 (tpt90) outliers start: 26 outliers final: 15 residues processed: 79 average time/residue: 0.1147 time to fit residues: 12.0693 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 123 ILE 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 207 MET Chi-restraints excluded: chain 1 residue 219 LEU Chi-restraints excluded: chain 1 residue 285 TYR Chi-restraints excluded: chain 1 residue 343 HIS Chi-restraints excluded: chain 1 residue 434 LEU Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 36 ILE Chi-restraints excluded: chain 2 residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.4810 r_free = 0.4810 target = 0.239708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.233294 restraints weight = 8232.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.231800 restraints weight = 9694.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.231405 restraints weight = 9859.810| |-----------------------------------------------------------------------------| r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5048 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3983 Z= 0.181 Angle : 0.701 10.446 5392 Z= 0.342 Chirality : 0.043 0.146 652 Planarity : 0.005 0.075 665 Dihedral : 4.969 27.619 541 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.09 % Favored : 91.49 % Rotamer: Outliers : 6.10 % Allowed : 24.63 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.36), residues: 470 helix: -0.03 (0.27), residues: 299 sheet: 0.09 (1.80), residues: 12 loop : -2.54 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP 1 379 HIS 0.002 0.001 HIS 1 360 PHE 0.013 0.001 PHE 1 458 TYR 0.013 0.002 TYR 1 272 ARG 0.003 0.001 ARG w 12 *********************** 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 83 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: 1 123 ILE cc_start: 0.4479 (OUTLIER) cc_final: 0.4269 (pt) REVERT: 1 191 ILE cc_start: 0.4928 (tp) cc_final: 0.4695 (tp) REVERT: 1 226 LYS cc_start: 0.0996 (OUTLIER) cc_final: 0.0450 (ptpt) REVERT: 1 243 MET cc_start: 0.6300 (tpt) cc_final: 0.3982 (mtt) REVERT: 1 268 LYS cc_start: 0.4372 (tttm) cc_final: 0.3500 (tttm) REVERT: 1 357 ASP cc_start: 0.2669 (OUTLIER) cc_final: 0.1485 (p0) REVERT: 1 434 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5431 (mt) REVERT: 2 20 ARG cc_start: 0.5659 (tpt170) cc_final: 0.4326 (mtt90) outliers start: 25 outliers final: 15 residues processed: 76 average time/residue: 0.1394 time to fit residues: 13.6166 Evaluate side-chains 71 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 ILE 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 226 LYS Chi-restraints excluded: chain 1 residue 256 ILE 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 427 CYS Chi-restraints excluded: chain 1 residue 434 LEU Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Chi-restraints excluded: chain 2 residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 43 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 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 = 0.4836 r_free = 0.4836 target = 0.241923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.235264 restraints weight = 7892.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.234978 restraints weight = 8574.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 91)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.234508 restraints weight = 7486.391| |-----------------------------------------------------------------------------| r_work (final): 0.4755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4938 moved from start: 0.6902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3983 Z= 0.160 Angle : 0.699 16.041 5392 Z= 0.333 Chirality : 0.041 0.143 652 Planarity : 0.004 0.071 665 Dihedral : 4.589 23.031 541 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.23 % Favored : 92.34 % Rotamer: Outliers : 3.90 % Allowed : 25.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.37), residues: 470 helix: 0.10 (0.28), residues: 303 sheet: 0.29 (1.87), residues: 12 loop : -2.47 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP 1 379 HIS 0.001 0.000 HIS 2 58 PHE 0.012 0.001 PHE 1 252 TYR 0.013 0.001 TYR 1 344 ARG 0.002 0.000 ARG 1 271 *********************** 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 72 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: 1 123 ILE cc_start: 0.4196 (OUTLIER) cc_final: 0.3869 (pt) REVERT: 1 179 ILE cc_start: 0.5668 (OUTLIER) cc_final: 0.5107 (tp) REVERT: 1 243 MET cc_start: 0.6189 (tpt) cc_final: 0.4149 (mtt) REVERT: 1 268 LYS cc_start: 0.4494 (tttm) cc_final: 0.3519 (tttm) REVERT: 2 20 ARG cc_start: 0.5596 (tpt170) cc_final: 0.4177 (mtt90) outliers start: 16 outliers final: 10 residues processed: 66 average time/residue: 0.1407 time to fit residues: 11.8815 Evaluate side-chains 63 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 ILE 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 207 MET Chi-restraints excluded: chain 1 residue 427 CYS Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4813 r_free = 0.4813 target = 0.239900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.233277 restraints weight = 8049.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.232458 restraints weight = 9030.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.231923 restraints weight = 8706.543| |-----------------------------------------------------------------------------| r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5028 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3983 Z= 0.178 Angle : 0.733 15.811 5392 Z= 0.353 Chirality : 0.042 0.139 652 Planarity : 0.004 0.068 665 Dihedral : 4.644 20.329 541 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.23 % Favored : 92.34 % Rotamer: Outliers : 4.15 % Allowed : 26.83 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.37), residues: 470 helix: 0.14 (0.28), residues: 303 sheet: 0.44 (1.85), residues: 12 loop : -2.50 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP 1 379 HIS 0.002 0.001 HIS 1 411 PHE 0.011 0.001 PHE 1 252 TYR 0.011 0.001 TYR 1 344 ARG 0.002 0.000 ARG 1 271 *********************** 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 74 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: 1 123 ILE cc_start: 0.4394 (OUTLIER) cc_final: 0.4172 (pt) REVERT: 1 243 MET cc_start: 0.6228 (tpt) cc_final: 0.4399 (mtt) REVERT: 1 268 LYS cc_start: 0.4629 (tttm) cc_final: 0.4195 (tmmt) REVERT: 1 357 ASP cc_start: 0.2842 (OUTLIER) cc_final: 0.1739 (p0) REVERT: 2 20 ARG cc_start: 0.5706 (tpt170) cc_final: 0.4271 (mtt90) outliers start: 17 outliers final: 13 residues processed: 70 average time/residue: 0.1563 time to fit residues: 13.7878 Evaluate side-chains 63 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 ILE 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 219 LEU Chi-restraints excluded: chain 1 residue 357 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.238649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.231041 restraints weight = 7806.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.229584 restraints weight = 9034.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.229162 restraints weight = 8248.218| |-----------------------------------------------------------------------------| r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5129 moved from start: 0.7436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3983 Z= 0.183 Angle : 0.733 15.754 5392 Z= 0.350 Chirality : 0.042 0.149 652 Planarity : 0.004 0.069 665 Dihedral : 4.633 22.826 541 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.66 % Favored : 91.91 % Rotamer: Outliers : 4.39 % Allowed : 25.61 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.37), residues: 470 helix: 0.18 (0.28), residues: 302 sheet: 0.41 (1.86), residues: 12 loop : -2.45 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP 1 379 HIS 0.002 0.001 HIS 1 360 PHE 0.012 0.001 PHE 1 252 TYR 0.012 0.002 TYR 1 344 ARG 0.002 0.000 ARG 1 405 *********************** 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 71 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.379 Fit side-chains REVERT: 1 123 ILE cc_start: 0.4333 (OUTLIER) cc_final: 0.4083 (pt) REVERT: 1 226 LYS cc_start: 0.1316 (OUTLIER) cc_final: 0.0739 (ptpt) REVERT: 1 243 MET cc_start: 0.6116 (tpt) cc_final: 0.4263 (mtt) REVERT: 1 268 LYS cc_start: 0.4613 (tttm) cc_final: 0.3274 (tttm) REVERT: 1 357 ASP cc_start: 0.3161 (OUTLIER) cc_final: 0.2171 (p0) REVERT: 2 20 ARG cc_start: 0.5641 (tpt170) cc_final: 0.4253 (mtt90) outliers start: 18 outliers final: 13 residues processed: 68 average time/residue: 0.1529 time to fit residues: 13.1295 Evaluate side-chains 68 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 ILE 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 219 LEU Chi-restraints excluded: chain 1 residue 226 LYS Chi-restraints excluded: chain 1 residue 357 ASP Chi-restraints excluded: chain 1 residue 374 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 40.0000 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 127 GLN 1 259 GLN ** 1 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 404 HIS 1 465 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.229834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.220872 restraints weight = 7928.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.219553 restraints weight = 12731.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.219765 restraints weight = 11497.143| |-----------------------------------------------------------------------------| r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.8161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3983 Z= 0.337 Angle : 0.927 16.398 5392 Z= 0.454 Chirality : 0.049 0.195 652 Planarity : 0.006 0.072 665 Dihedral : 6.273 37.029 541 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.51 % Favored : 90.64 % Rotamer: Outliers : 4.88 % Allowed : 26.10 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.35), residues: 470 helix: -0.42 (0.27), residues: 301 sheet: -0.55 (1.69), residues: 12 loop : -2.94 (0.43), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.006 TRP 1 379 HIS 0.008 0.002 HIS 1 360 PHE 0.016 0.002 PHE 2 49 TYR 0.022 0.003 TYR 1 272 ARG 0.005 0.001 ARG 2 30 *********************** 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 77 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.467 Fit side-chains REVERT: 1 188 CYS cc_start: 0.4245 (OUTLIER) cc_final: 0.3416 (m) REVERT: 1 207 MET cc_start: 0.3711 (OUTLIER) cc_final: 0.2074 (mmm) REVERT: 1 226 LYS cc_start: 0.3501 (OUTLIER) cc_final: 0.2080 (ptpt) REVERT: 1 357 ASP cc_start: 0.3307 (OUTLIER) cc_final: 0.2301 (p0) REVERT: 2 20 ARG cc_start: 0.5740 (tpt170) cc_final: 0.4047 (mtt90) outliers start: 20 outliers final: 13 residues processed: 73 average time/residue: 0.1501 time to fit residues: 14.1473 Evaluate side-chains 65 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 259 GLN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.234769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.226526 restraints weight = 8132.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.224917 restraints weight = 10773.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.224853 restraints weight = 10938.629| |-----------------------------------------------------------------------------| r_work (final): 0.4647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 moved from start: 0.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3983 Z= 0.189 Angle : 0.792 14.696 5392 Z= 0.383 Chirality : 0.043 0.135 652 Planarity : 0.005 0.074 665 Dihedral : 5.192 29.513 541 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.23 % Favored : 92.13 % Rotamer: Outliers : 2.44 % Allowed : 28.54 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.36), residues: 470 helix: -0.07 (0.28), residues: 303 sheet: -0.23 (1.75), residues: 12 loop : -2.74 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP 1 379 HIS 0.002 0.001 HIS 1 411 PHE 0.019 0.001 PHE 1 252 TYR 0.015 0.002 TYR 1 344 ARG 0.002 0.000 ARG 1 271 ********************** 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 62 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.423 Fit side-chains REVERT: 1 133 MET cc_start: 0.5260 (ppp) cc_final: 0.4946 (ppp) REVERT: 1 207 MET cc_start: 0.2997 (OUTLIER) cc_final: 0.1481 (mmm) REVERT: 1 268 LYS cc_start: 0.4609 (tttm) cc_final: 0.3644 (tttp) REVERT: 2 20 ARG cc_start: 0.5447 (tpt170) cc_final: 0.4122 (mtt90) outliers start: 10 outliers final: 9 residues processed: 59 average time/residue: 0.1669 time to fit residues: 12.3228 Evaluate side-chains 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 427 CYS Chi-restraints excluded: chain 1 residue 448 LEU Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 0.0000 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 overall best weight: 3.1390 ------------------------------------------------------------------------------- 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 = 0.4733 r_free = 0.4733 target = 0.232923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.225268 restraints weight = 7903.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.223984 restraints weight = 10443.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.223684 restraints weight = 9420.353| |-----------------------------------------------------------------------------| r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 moved from start: 0.8425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3983 Z= 0.222 Angle : 0.792 14.621 5392 Z= 0.383 Chirality : 0.044 0.148 652 Planarity : 0.005 0.069 665 Dihedral : 5.215 30.350 541 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.51 % Favored : 90.85 % Rotamer: Outliers : 2.68 % Allowed : 28.05 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.37), residues: 470 helix: -0.07 (0.28), residues: 305 sheet: -0.37 (1.72), residues: 12 loop : -2.76 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.006 TRP 1 379 HIS 0.004 0.001 HIS 1 360 PHE 0.018 0.002 PHE 1 252 TYR 0.016 0.002 TYR 1 272 ARG 0.002 0.001 ARG w 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1527.90 seconds wall clock time: 27 minutes 11.16 seconds (1631.16 seconds total)