Starting phenix.real_space_refine on Mon Nov 13 18:21:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/11_2023/3jc2_3245.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/11_2023/3jc2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/11_2023/3jc2_3245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/11_2023/3jc2_3245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/11_2023/3jc2_3245.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/11_2023/3jc2_3245.pdb" } 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 Residue "1 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 381": "OE1" <-> "OE2" Residue "1 ARG 405": "NH1" <-> "NH2" Residue "1 PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 2.65, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 837.0 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: 0.35 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: 0.90 Time building geometry restraints manager: 1.65 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: 93.71 - 103.66: 45 103.66 - 113.62: 2114 113.62 - 123.57: 3005 123.57 - 133.52: 223 133.52 - 143.48: 5 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 2.520 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 2.520 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 ========== 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: 3.250 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: 14.550 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.110 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.740 ------------------------------------------------------------------------------- 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 *********************** 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 fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.423 Fit side-chains outliers start: 30 outliers final: 7 residues processed: 134 average time/residue: 0.1719 time to fit residues: 27.9208 Evaluate side-chains 71 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.0355 time to fit residues: 0.9353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3983 Z= 0.235 Angle : 0.829 9.490 5392 Z= 0.413 Chirality : 0.046 0.200 652 Planarity : 0.007 0.104 665 Dihedral : 5.729 22.374 541 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.87 % Favored : 91.28 % Rotamer: Outliers : 5.85 % Allowed : 15.37 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.62 (0.35), residues: 470 helix: -1.07 (0.27), residues: 293 sheet: -0.93 (1.41), residues: 12 loop : -2.92 (0.46), residues: 165 *********************** 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 fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.442 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 100 average time/residue: 0.1354 time to fit residues: 17.3835 Evaluate side-chains 71 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0437 time to fit residues: 1.4087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 40 optimal weight: 0.0040 chunk 15 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3983 Z= 0.250 Angle : 0.796 12.060 5392 Z= 0.388 Chirality : 0.045 0.217 652 Planarity : 0.006 0.089 665 Dihedral : 5.646 34.708 541 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.51 % Favored : 90.85 % Rotamer: Outliers : 3.66 % Allowed : 20.98 % Favored : 75.37 % 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: -1.66 (0.37), residues: 470 helix: -0.31 (0.28), residues: 292 sheet: 0.01 (1.66), residues: 12 loop : -2.59 (0.47), residues: 166 *********************** 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 78 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.436 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 73 average time/residue: 0.1326 time to fit residues: 12.6739 Evaluate side-chains 59 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0386 time to fit residues: 0.9525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 chunk 48 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 186 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 3983 Z= 0.210 Angle : 0.738 10.413 5392 Z= 0.361 Chirality : 0.045 0.232 652 Planarity : 0.005 0.087 665 Dihedral : 5.280 29.884 541 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.45 % Favored : 91.91 % Rotamer: Outliers : 3.41 % Allowed : 24.39 % Favored : 72.20 % 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: -1.30 (0.37), residues: 470 helix: -0.01 (0.28), residues: 301 sheet: 0.47 (1.80), residues: 12 loop : -2.60 (0.46), residues: 157 *********************** 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 73 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.448 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 68 average time/residue: 0.1272 time to fit residues: 11.5067 Evaluate side-chains 56 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0759 time to fit residues: 1.2040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- 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** 1 404 HIS 1 414 ASN ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 3983 Z= 0.294 Angle : 0.812 11.767 5392 Z= 0.401 Chirality : 0.045 0.249 652 Planarity : 0.006 0.084 665 Dihedral : 5.742 34.796 541 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.87 % Favored : 91.28 % Rotamer: Outliers : 3.90 % Allowed : 24.39 % 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 (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: -1.59 (0.37), residues: 470 helix: -0.17 (0.28), residues: 297 sheet: -0.56 (1.68), residues: 12 loop : -2.73 (0.44), residues: 161 *********************** 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 78 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.376 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 70 average time/residue: 0.1188 time to fit residues: 11.1084 Evaluate side-chains 59 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0395 time to fit residues: 1.0928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 30.0000 chunk 25 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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** 2 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.7550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 3983 Z= 0.215 Angle : 0.730 10.760 5392 Z= 0.360 Chirality : 0.042 0.138 652 Planarity : 0.005 0.079 665 Dihedral : 5.454 37.126 541 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.23 % Favored : 91.91 % Rotamer: Outliers : 1.95 % Allowed : 27.80 % 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 (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: -1.57 (0.37), residues: 470 helix: -0.10 (0.29), residues: 297 sheet: -0.84 (1.55), residues: 12 loop : -2.83 (0.44), residues: 161 *********************** 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 64 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.440 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.1507 time to fit residues: 11.8594 Evaluate side-chains 59 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0521 time to fit residues: 1.0570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.0270 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- 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** ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.8044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 3983 Z= 0.270 Angle : 0.792 11.386 5392 Z= 0.388 Chirality : 0.043 0.147 652 Planarity : 0.005 0.074 665 Dihedral : 5.696 35.623 541 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.45 % Favored : 91.70 % Rotamer: Outliers : 2.68 % Allowed : 26.83 % 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: -1.78 (0.36), residues: 470 helix: -0.22 (0.29), residues: 295 sheet: -1.31 (1.51), residues: 12 loop : -2.95 (0.43), residues: 163 *********************** 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 69 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.401 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 0.1444 time to fit residues: 12.1187 Evaluate side-chains 55 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0387 time to fit residues: 0.8682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.8556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 3983 Z= 0.297 Angle : 0.832 11.947 5392 Z= 0.405 Chirality : 0.045 0.150 652 Planarity : 0.005 0.077 665 Dihedral : 5.921 34.529 541 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.85 % Allowed : 6.38 % Favored : 92.77 % Rotamer: Outliers : 1.46 % Allowed : 29.51 % 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: -2.01 (0.36), residues: 470 helix: -0.41 (0.28), residues: 292 sheet: -1.41 (1.51), residues: 12 loop : -2.98 (0.42), residues: 166 *********************** 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 60 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.428 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.1503 time to fit residues: 10.8341 Evaluate side-chains 54 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0384 time to fit residues: 0.7194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 40.0000 chunk 28 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.8716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3983 Z= 0.201 Angle : 0.752 10.674 5392 Z= 0.360 Chirality : 0.042 0.156 652 Planarity : 0.004 0.069 665 Dihedral : 5.381 32.731 541 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.23 % Favored : 92.13 % Rotamer: Outliers : 0.98 % Allowed : 29.76 % 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: -1.72 (0.36), residues: 470 helix: -0.21 (0.28), residues: 304 sheet: -1.19 (1.50), residues: 12 loop : -2.99 (0.44), residues: 154 *********************** 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 63 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.426 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 62 average time/residue: 0.1606 time to fit residues: 12.6904 Evaluate side-chains 56 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.8850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3983 Z= 0.244 Angle : 0.794 11.369 5392 Z= 0.383 Chirality : 0.043 0.150 652 Planarity : 0.005 0.063 665 Dihedral : 5.522 33.380 541 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.81 % Favored : 92.55 % Rotamer: Outliers : 0.73 % Allowed : 31.95 % Favored : 67.32 % 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: -1.64 (0.37), residues: 470 helix: -0.11 (0.28), residues: 301 sheet: -0.99 (1.52), residues: 12 loop : -3.01 (0.45), residues: 157 ********************** 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 58 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.419 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.1495 time to fit residues: 10.9858 Evaluate side-chains 56 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0390 time to fit residues: 0.7912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- 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 = 0.4714 r_free = 0.4714 target = 0.230993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.224575 restraints weight = 8093.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.223987 restraints weight = 10712.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.223111 restraints weight = 10650.088| |-----------------------------------------------------------------------------| r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.8978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3983 Z= 0.216 Angle : 0.768 11.319 5392 Z= 0.368 Chirality : 0.043 0.145 652 Planarity : 0.004 0.058 665 Dihedral : 5.353 32.837 541 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.45 % Favored : 91.91 % Rotamer: Outliers : 0.49 % Allowed : 31.71 % Favored : 67.80 % 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: -1.41 (0.37), residues: 470 helix: 0.08 (0.29), residues: 301 sheet: -1.16 (1.46), residues: 12 loop : -2.92 (0.46), residues: 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1065.45 seconds wall clock time: 20 minutes 9.26 seconds (1209.26 seconds total)