Starting phenix.real_space_refine (version: dev) on Thu May 12 14:37:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/05_2022/3jc2_3245.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/05_2022/3jc2_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_3245/05_2022/3jc2_3245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/05_2022/3jc2_3245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/05_2022/3jc2_3245.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc2_3245/05_2022/3jc2_3245.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4597/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: 2.81, per 1000 atoms: 0.72 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: 1.60 Conformation dependent library (CDL) restraints added in 713.4 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: 0.16 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: 0.97 Time building geometry restraints manager: 1.74 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 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. 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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 13.080 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 16.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 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 % 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 : 0.350 Fit side-chains outliers start: 30 outliers final: 5 residues processed: 134 average time/residue: 0.1648 time to fit residues: 26.8575 Evaluate side-chains 68 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0373 time to fit residues: 0.9319 ------------------------------------------------------------------------------- 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: 9.9990 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- 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 1 393 GLN ** 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: 0.5936 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.099 3983 Z= 0.370 Angle : 0.956 10.954 5392 Z= 0.478 Chirality : 0.050 0.207 652 Planarity : 0.007 0.111 665 Dihedral : 6.161 27.024 541 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 1.28 % Allowed : 7.66 % Favored : 91.06 % Rotamer Outliers : 6.83 % 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: -2.72 (0.35), residues: 470 helix: -1.13 (0.27), residues: 293 sheet: -0.57 (1.56), residues: 12 loop : -3.04 (0.45), 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 107 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 0.466 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 102 average time/residue: 0.1386 time to fit residues: 18.1043 Evaluate side-chains 71 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0443 time to fit residues: 1.6653 ------------------------------------------------------------------------------- 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: 6.9990 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 40 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5946 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 3983 Z= 0.249 Angle : 0.847 14.618 5392 Z= 0.414 Chirality : 0.045 0.234 652 Planarity : 0.006 0.086 665 Dihedral : 5.670 36.364 541 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.09 % Favored : 91.06 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.86 (0.36), residues: 470 helix: -0.40 (0.28), residues: 291 sheet: -0.30 (1.58), residues: 12 loop : -2.76 (0.46), residues: 167 *********************** 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 82 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.446 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 77 average time/residue: 0.1325 time to fit residues: 13.2868 Evaluate side-chains 62 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0420 time to fit residues: 1.2093 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5937 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 3983 Z= 0.217 Angle : 0.773 13.598 5392 Z= 0.387 Chirality : 0.044 0.281 652 Planarity : 0.005 0.080 665 Dihedral : 5.327 31.188 541 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.45 % Favored : 91.91 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.29), residues: 295 sheet: 0.38 (1.82), residues: 12 loop : -2.66 (0.45), residues: 163 *********************** 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 68 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.449 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.1460 time to fit residues: 12.0307 Evaluate side-chains 57 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0546 time to fit residues: 1.1789 ------------------------------------------------------------------------------- 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: 10.0000 chunk 19 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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: 0.5947 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.123 3983 Z= 0.239 Angle : 0.762 10.902 5392 Z= 0.380 Chirality : 0.043 0.155 652 Planarity : 0.005 0.071 665 Dihedral : 5.321 32.038 541 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.02 % Favored : 92.13 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.40 (0.37), residues: 470 helix: -0.01 (0.28), residues: 300 sheet: -0.04 (1.82), residues: 12 loop : -2.77 (0.45), residues: 158 *********************** 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 68 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.460 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 66 average time/residue: 0.1441 time to fit residues: 12.3161 Evaluate side-chains 56 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0408 time to fit residues: 1.0703 ------------------------------------------------------------------------------- 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: 7.9990 chunk 48 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 35 optimal weight: 0.4980 overall best weight: 4.8988 ------------------------------------------------------------------------------- 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** ** 1 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6018 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.113 3983 Z= 0.317 Angle : 0.901 16.128 5392 Z= 0.456 Chirality : 0.045 0.176 652 Planarity : 0.006 0.067 665 Dihedral : 5.805 30.833 541 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.66 % Favored : 91.49 % Rotamer Outliers : 2.68 % 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: -1.77 (0.36), residues: 470 helix: -0.28 (0.28), residues: 301 sheet: -1.15 (1.54), residues: 12 loop : -2.88 (0.44), residues: 157 *********************** 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 70 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.433 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.1311 time to fit residues: 11.2983 Evaluate side-chains 55 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0434 time to fit residues: 0.9483 ------------------------------------------------------------------------------- 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: 9.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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: 0.6034 moved from start: 0.7981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.242 3983 Z= 0.348 Angle : 0.893 15.808 5392 Z= 0.457 Chirality : 0.045 0.185 652 Planarity : 0.006 0.089 665 Dihedral : 5.926 35.755 541 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.66 % Favored : 91.49 % Rotamer Outliers : 1.22 % 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 (0.36), residues: 470 helix: -0.32 (0.28), residues: 294 sheet: -1.37 (1.53), residues: 12 loop : -2.97 (0.42), residues: 164 *********************** 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 55 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.450 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.1461 time to fit residues: 10.0492 Evaluate side-chains 50 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0367 time to fit residues: 0.6768 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 0.0070 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- 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: 0.6031 moved from start: 0.8018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.017 0.775 3983 Z= 0.663 Angle : 1.819 106.033 5392 Z= 0.726 Chirality : 0.045 0.225 652 Planarity : 0.006 0.065 665 Dihedral : 5.911 35.758 541 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.87 % Favored : 91.28 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.21 % 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: -1.89 (0.36), residues: 470 helix: -0.32 (0.28), residues: 294 sheet: -1.41 (1.52), residues: 12 loop : -2.96 (0.42), residues: 164 *********************** 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 51 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.460 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 49 average time/residue: 0.1524 time to fit residues: 9.7422 Evaluate side-chains 47 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0668 time to fit residues: 0.7224 ------------------------------------------------------------------------------- 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: 0.0050 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 50.0000 chunk 47 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 45 optimal weight: 0.4980 chunk 39 optimal weight: 6.9990 overall best weight: 1.8998 ------------------------------------------------------------------------------- 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: 0.6028 moved from start: 0.8042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.017 0.776 3983 Z= 0.662 Angle : 1.819 106.100 5392 Z= 0.726 Chirality : 0.045 0.220 652 Planarity : 0.006 0.065 665 Dihedral : 5.911 35.758 541 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.87 % Favored : 91.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.21 % 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: -1.89 (0.36), residues: 470 helix: -0.32 (0.28), residues: 294 sheet: -1.41 (1.52), residues: 12 loop : -2.96 (0.42), residues: 164 *********************** 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 46 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.474 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1546 time to fit residues: 9.2612 Evaluate side-chains 46 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6158 ------------------------------------------------------------------------------- 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: 6.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 42 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 overall best weight: 3.3504 ------------------------------------------------------------------------------- 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: 0.6029 moved from start: 0.8043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.017 0.776 3983 Z= 0.662 Angle : 1.819 106.100 5392 Z= 0.726 Chirality : 0.045 0.220 652 Planarity : 0.006 0.065 665 Dihedral : 5.911 35.758 541 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.87 % Favored : 91.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.21 % 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: -1.89 (0.36), residues: 470 helix: -0.32 (0.28), residues: 294 sheet: -1.41 (1.52), residues: 12 loop : -2.96 (0.42), residues: 164 ********************** 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 46 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.628 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1602 time to fit residues: 9.6266 Evaluate side-chains 46 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6495 ------------------------------------------------------------------------------- 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: 8.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.230711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.224410 restraints weight = 8024.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.223107 restraints weight = 7323.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.223002 restraints weight = 6421.410| |-----------------------------------------------------------------------------| r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5339 moved from start: 0.8043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.017 0.776 3983 Z= 0.662 Angle : 1.819 106.100 5392 Z= 0.726 Chirality : 0.045 0.220 652 Planarity : 0.006 0.065 665 Dihedral : 5.911 35.758 541 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.87 % Favored : 91.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.21 % 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: -1.89 (0.36), residues: 470 helix: -0.32 (0.28), residues: 294 sheet: -1.41 (1.52), residues: 12 loop : -2.96 (0.42), residues: 164 =============================================================================== Job complete usr+sys time: 1007.23 seconds wall clock time: 19 minutes 2.20 seconds (1142.20 seconds total)