Starting phenix.real_space_refine on Tue Dec 12 09:37:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/12_2023/8d45_27175.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/12_2023/8d45_27175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/12_2023/8d45_27175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/12_2023/8d45_27175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/12_2023/8d45_27175.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/12_2023/8d45_27175.pdb" } resolution = 2.62 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= -0.000 sd= 0.052 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 6716 2.51 5 N 1846 2.21 5 O 1944 1.98 5 H 10370 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 317": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20932 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5225 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 bond proxies already assigned to first conformer: 5239 Chain: "B" Number of atoms: 5225 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 bond proxies already assigned to first conformer: 5239 Chain: "C" Number of atoms: 5225 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 bond proxies already assigned to first conformer: 5239 Chain: "D" Number of atoms: 5257 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 5233 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 318} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 341, 5233 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 318} Chain breaks: 2 bond proxies already assigned to first conformer: 5272 Time building chain proxies: 16.33, per 1000 atoms: 0.78 Number of scatterers: 20932 At special positions: 0 Unit cell: (103.79, 63.13, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 1944 8.00 N 1846 7.00 C 6716 6.00 H 10370 1.00 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: 17.81 Conformation dependent library (CDL) restraints added in 4.5 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 54.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 52 through 67 Processing helix chain 'A' and resid 96 through 113 removed outlier: 3.752A pdb=" N ASN A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 152 removed outlier: 3.906A pdb=" N VAL A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.700A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 220 through 239 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.853A pdb=" N ASP A 263 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.739A pdb=" N ARG A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 332 through 338 removed outlier: 4.006A pdb=" N MET A 337 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 96 through 112 Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.871A pdb=" N VAL B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 3.535A pdb=" N ALA B 167 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 209 Processing helix chain 'B' and resid 222 through 239 Processing helix chain 'B' and resid 277 through 292 removed outlier: 4.011A pdb=" N ARG B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.959A pdb=" N MET B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 348 through 355 removed outlier: 3.515A pdb=" N TRP B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 19 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.708A pdb=" N GLU C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 96 through 113 removed outlier: 3.644A pdb=" N ASN C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 152 removed outlier: 3.902A pdb=" N VAL C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 3.659A pdb=" N ALA C 167 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 209 Processing helix chain 'C' and resid 222 through 238 Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.000A pdb=" N ARG C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 322 through 328 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.536A pdb=" N ASP C 336 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 348 through 355 removed outlier: 3.574A pdb=" N TRP C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 52 through 67 Processing helix chain 'D' and resid 96 through 112 Processing helix chain 'D' and resid 134 through 152 removed outlier: 3.871A pdb=" N VAL D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 148 " --> pdb=" O GLN D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 removed outlier: 3.557A pdb=" N ALA D 167 " --> pdb=" O HIS D 163 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 220 through 238 Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.845A pdb=" N ILE D 262 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP D 263 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 4.009A pdb=" N ARG D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Proline residue: D 316 - end of helix Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.922A pdb=" N MET D 337 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 348 through 355 removed outlier: 3.697A pdb=" N TRP D 352 " --> pdb=" O ARG D 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 123 removed outlier: 5.833A pdb=" N VAL A 122 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 72 removed outlier: 3.569A pdb=" N ALA B 119 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 244 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.619A pdb=" N LEU C 156 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR C 184 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA C 158 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 70 through 72 518 hydrogen bonds defined for protein. 1440 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: 7.64 Time building geometry restraints manager: 18.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 10342 1.02 - 1.22: 33 1.22 - 1.42: 4492 1.42 - 1.61: 6246 1.61 - 1.81: 84 Bond restraints: 21197 Sorted by residual: bond pdb=" NE ARG B 108 " pdb=" HE ARG B 108 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C TRP B 44 " pdb=" N THR B 45 " ideal model delta sigma weight residual 1.331 1.384 -0.053 2.07e-02 2.33e+03 6.62e+00 bond pdb=" C TRP C 44 " pdb=" N THR C 45 " ideal model delta sigma weight residual 1.331 1.378 -0.047 2.07e-02 2.33e+03 5.09e+00 bond pdb=" N THR B 222 " pdb=" CA THR B 222 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.25e-02 6.40e+03 4.23e+00 bond pdb=" N THR C 222 " pdb=" CA THR C 222 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.27e-02 6.20e+03 3.26e+00 ... (remaining 21192 not shown) Histogram of bond angle deviations from ideal: 97.73 - 104.98: 292 104.98 - 112.24: 24061 112.24 - 119.49: 5709 119.49 - 126.75: 8125 126.75 - 134.00: 205 Bond angle restraints: 38392 Sorted by residual: angle pdb=" CG LYS A 139 " pdb=" CD LYS A 139 " pdb=" CE LYS A 139 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N ASN A 152 " pdb=" CA ASN A 152 " pdb=" C ASN A 152 " ideal model delta sigma weight residual 110.91 107.56 3.35 1.17e+00 7.31e-01 8.18e+00 angle pdb=" N ARG A 239 " pdb=" CA ARG A 239 " pdb=" C ARG A 239 " ideal model delta sigma weight residual 111.24 107.32 3.92 1.38e+00 5.25e-01 8.09e+00 angle pdb=" N ARG B 239 " pdb=" CA ARG B 239 " pdb=" C ARG B 239 " ideal model delta sigma weight residual 111.24 107.40 3.84 1.38e+00 5.25e-01 7.74e+00 angle pdb=" N ASN C 152 " pdb=" CA ASN C 152 " pdb=" C ASN C 152 " ideal model delta sigma weight residual 110.91 107.68 3.23 1.17e+00 7.31e-01 7.63e+00 ... (remaining 38387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8420 17.62 - 35.24: 861 35.24 - 52.87: 260 52.87 - 70.49: 46 70.49 - 88.11: 27 Dihedral angle restraints: 9614 sinusoidal: 5047 harmonic: 4567 Sorted by residual: dihedral pdb=" CA ASP C 336 " pdb=" C ASP C 336 " pdb=" N MET C 337 " pdb=" CA MET C 337 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE C 74 " pdb=" C PHE C 74 " pdb=" N THR C 75 " pdb=" CA THR C 75 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE D 74 " pdb=" C PHE D 74 " pdb=" N THR D 75 " pdb=" CA THR D 75 " ideal model delta harmonic sigma weight residual 180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 9611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 853 0.029 - 0.058: 422 0.058 - 0.087: 176 0.087 - 0.115: 80 0.115 - 0.144: 23 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA PRO A 46 " pdb=" N PRO A 46 " pdb=" C PRO A 46 " pdb=" CB PRO A 46 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA PRO B 46 " pdb=" N PRO B 46 " pdb=" C PRO B 46 " pdb=" CB PRO B 46 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL A 196 " pdb=" N VAL A 196 " pdb=" C VAL A 196 " pdb=" CB VAL A 196 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1551 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 109 " -0.077 2.00e-02 2.50e+03 8.49e-02 1.08e+02 pdb=" CD GLN B 109 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN B 109 " 0.077 2.00e-02 2.50e+03 pdb=" NE2 GLN B 109 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN B 109 " 0.125 2.00e-02 2.50e+03 pdb="HE22 GLN B 109 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 315 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO D 316 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 316 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 316 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 315 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO C 316 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 316 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 316 " -0.040 5.00e-02 4.00e+02 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1588 2.21 - 2.81: 45468 2.81 - 3.41: 62571 3.41 - 4.00: 84710 4.00 - 4.60: 129854 Nonbonded interactions: 324191 Sorted by model distance: nonbonded pdb=" H ALA C 158 " pdb=" O ALA C 182 " model vdw 1.613 1.850 nonbonded pdb=" O ALA C 158 " pdb=" H THR C 184 " model vdw 1.626 1.850 nonbonded pdb=" O ILE D 24 " pdb=" H ASN D 69 " model vdw 1.686 1.850 nonbonded pdb=" O ILE A 357 " pdb="HD22 ASN B 364 " model vdw 1.686 1.850 nonbonded pdb=" O ILE B 24 " pdb=" H ASN B 69 " model vdw 1.700 1.850 ... (remaining 324186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 14 or resid 16 through 325 or resid 327 through \ 372)) selection = (chain 'B' and (resid 9 through 14 or resid 16 through 325 or resid 327 through \ 372)) selection = (chain 'C' and (resid 9 through 14 or resid 16 through 325 or resid 327 through \ 372)) selection = (chain 'D' and (resid 9 through 14 or resid 16 through 127 or resid 134 through \ 325 or resid 327 through 372)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.300 Extract box with map and model: 7.190 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 79.690 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.004 0.053 10827 Z= 0.288 Angle : 0.788 7.348 14666 Z= 0.445 Chirality : 0.044 0.144 1554 Planarity : 0.007 0.072 1935 Dihedral : 17.508 88.110 4022 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.92 % Allowed : 18.26 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1342 helix: -0.69 (0.19), residues: 676 sheet: -1.97 (0.32), residues: 132 loop : -0.76 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 342 HIS 0.007 0.002 HIS A 306 PHE 0.034 0.003 PHE B 155 TYR 0.016 0.002 TYR C 295 ARG 0.009 0.001 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 145 average time/residue: 1.9835 time to fit residues: 320.1530 Evaluate side-chains 138 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 2.0816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 290 ASN B 152 ASN B 290 ASN C 152 ASN C 354 ASN D 152 ASN D 290 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10827 Z= 0.315 Angle : 0.664 5.000 14666 Z= 0.347 Chirality : 0.043 0.148 1554 Planarity : 0.007 0.061 1935 Dihedral : 4.785 20.987 1475 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.94 % Allowed : 15.87 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.21 (0.22), residues: 1342 helix: -0.44 (0.19), residues: 652 sheet: -2.14 (0.32), residues: 130 loop : -0.70 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 342 HIS 0.009 0.002 HIS A 306 PHE 0.013 0.002 PHE D 141 TYR 0.018 0.002 TYR B 295 ARG 0.006 0.001 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 145 average time/residue: 2.0441 time to fit residues: 328.1578 Evaluate side-chains 139 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.636 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.7292 time to fit residues: 4.8432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 41 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10827 Z= 0.218 Angle : 0.594 4.882 14666 Z= 0.307 Chirality : 0.041 0.139 1554 Planarity : 0.005 0.052 1935 Dihedral : 4.485 17.770 1475 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.11 % Allowed : 16.24 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.62 (0.23), residues: 1342 helix: 0.13 (0.20), residues: 650 sheet: -2.20 (0.33), residues: 138 loop : -0.38 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.005 0.001 HIS B 338 PHE 0.012 0.002 PHE D 31 TYR 0.013 0.002 TYR B 295 ARG 0.002 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 144 average time/residue: 1.9845 time to fit residues: 317.3946 Evaluate side-chains 132 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.6897 time to fit residues: 5.6026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10827 Z= 0.250 Angle : 0.598 4.732 14666 Z= 0.308 Chirality : 0.042 0.139 1554 Planarity : 0.005 0.048 1935 Dihedral : 4.435 18.727 1475 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.48 % Allowed : 16.06 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.58 (0.23), residues: 1342 helix: 0.16 (0.20), residues: 657 sheet: -2.20 (0.33), residues: 138 loop : -0.34 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.006 0.002 HIS C 60 PHE 0.012 0.002 PHE A 261 TYR 0.017 0.002 TYR B 295 ARG 0.002 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 150 average time/residue: 1.9568 time to fit residues: 327.2968 Evaluate side-chains 140 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.683 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.6219 time to fit residues: 6.2493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10827 Z= 0.331 Angle : 0.638 5.055 14666 Z= 0.331 Chirality : 0.043 0.152 1554 Planarity : 0.006 0.088 1935 Dihedral : 4.552 19.942 1475 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.30 % Allowed : 15.87 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.82 (0.22), residues: 1342 helix: -0.02 (0.19), residues: 657 sheet: -2.19 (0.33), residues: 133 loop : -0.54 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.008 0.002 HIS C 60 PHE 0.017 0.003 PHE A 261 TYR 0.023 0.003 TYR C 295 ARG 0.005 0.001 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 12 residues processed: 153 average time/residue: 1.9915 time to fit residues: 337.6373 Evaluate side-chains 138 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.630 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.7792 time to fit residues: 4.9732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN D 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10827 Z= 0.337 Angle : 0.645 5.431 14666 Z= 0.335 Chirality : 0.044 0.152 1554 Planarity : 0.006 0.089 1935 Dihedral : 4.601 20.661 1475 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.75 % Allowed : 16.70 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.74 (0.22), residues: 1342 helix: 0.03 (0.20), residues: 636 sheet: -2.23 (0.33), residues: 133 loop : -0.45 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 279 HIS 0.008 0.002 HIS C 60 PHE 0.018 0.003 PHE A 261 TYR 0.025 0.002 TYR B 295 ARG 0.012 0.001 ARG D 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 152 average time/residue: 2.0624 time to fit residues: 347.2635 Evaluate side-chains 141 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.781 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.3869 time to fit residues: 3.3090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 80 optimal weight: 0.2980 chunk 78 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10827 Z= 0.197 Angle : 0.572 5.623 14666 Z= 0.293 Chirality : 0.041 0.138 1554 Planarity : 0.005 0.085 1935 Dihedral : 4.273 19.715 1475 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.47 % Allowed : 17.52 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.10 (0.23), residues: 1342 helix: 0.65 (0.20), residues: 635 sheet: -2.33 (0.34), residues: 133 loop : -0.13 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 279 HIS 0.005 0.001 HIS A 52 PHE 0.018 0.002 PHE D 31 TYR 0.012 0.001 TYR B 295 ARG 0.009 0.000 ARG D 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 143 average time/residue: 2.0359 time to fit residues: 324.5991 Evaluate side-chains 130 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.791 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.4129 time to fit residues: 2.9472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 364 ASN D 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10827 Z= 0.372 Angle : 0.657 5.802 14666 Z= 0.342 Chirality : 0.044 0.155 1554 Planarity : 0.007 0.083 1935 Dihedral : 4.565 20.984 1475 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.83 % Allowed : 17.89 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.62 (0.23), residues: 1342 helix: 0.12 (0.20), residues: 636 sheet: -2.28 (0.33), residues: 133 loop : -0.34 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 279 HIS 0.009 0.002 HIS C 60 PHE 0.020 0.003 PHE D 261 TYR 0.025 0.003 TYR B 295 ARG 0.011 0.001 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 143 average time/residue: 2.1540 time to fit residues: 340.4741 Evaluate side-chains 135 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.660 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 2.1160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 126 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10827 Z= 0.206 Angle : 0.587 6.478 14666 Z= 0.301 Chirality : 0.041 0.139 1554 Planarity : 0.006 0.084 1935 Dihedral : 4.349 19.923 1475 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.10 % Allowed : 18.62 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.14 (0.23), residues: 1342 helix: 0.58 (0.20), residues: 635 sheet: -2.33 (0.34), residues: 133 loop : -0.11 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 279 HIS 0.004 0.001 HIS C 60 PHE 0.018 0.002 PHE B 31 TYR 0.013 0.002 TYR B 295 ARG 0.011 0.000 ARG D 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 134 average time/residue: 2.1712 time to fit residues: 320.6589 Evaluate side-chains 129 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.787 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 2.0785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 121 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10827 Z= 0.198 Angle : 0.580 6.889 14666 Z= 0.294 Chirality : 0.041 0.139 1554 Planarity : 0.005 0.078 1935 Dihedral : 4.199 19.473 1475 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.19 % Allowed : 18.90 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.09 (0.24), residues: 1342 helix: 0.81 (0.21), residues: 635 sheet: -2.35 (0.34), residues: 133 loop : 0.01 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.005 0.001 HIS C 60 PHE 0.017 0.002 PHE B 148 TYR 0.013 0.001 TYR B 295 ARG 0.005 0.000 ARG B 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 135 average time/residue: 1.9758 time to fit residues: 296.0563 Evaluate side-chains 131 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 2.1478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.180256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140966 restraints weight = 55638.651| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.85 r_work: 0.3684 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10827 Z= 0.231 Angle : 0.588 6.586 14666 Z= 0.300 Chirality : 0.041 0.139 1554 Planarity : 0.005 0.082 1935 Dihedral : 4.242 19.954 1475 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.10 % Allowed : 18.99 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.01 (0.23), residues: 1342 helix: 0.73 (0.20), residues: 635 sheet: -2.31 (0.35), residues: 133 loop : -0.06 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 279 HIS 0.006 0.001 HIS C 60 PHE 0.017 0.002 PHE B 261 TYR 0.016 0.002 TYR B 295 ARG 0.006 0.000 ARG B 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7724.70 seconds wall clock time: 136 minutes 10.92 seconds (8170.92 seconds total)