Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:37:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/02_2023/7pim_13442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/02_2023/7pim_13442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/02_2023/7pim_13442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/02_2023/7pim_13442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/02_2023/7pim_13442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pim_13442/02_2023/7pim_13442_updated.pdb" } resolution = 4.6 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= 0.000 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "G" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "D" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "E" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "F" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "H" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.98, per 1000 atoms: 0.59 Number of scatterers: 11844 At special positions: 0 Unit cell: (103.984, 91.12, 121.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 36 16.00 O 2156 8.00 N 1932 7.00 C 7192 6.00 H 524 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: 5.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 16 sheets defined 53.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 249 through 261 removed outlier: 3.593A pdb=" N GLU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 336 through 339 No H-bonds generated for 'chain 'B' and resid 336 through 339' Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 360 through 373 removed outlier: 3.523A pdb=" N TYR B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.911A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 472 through 495 removed outlier: 3.540A pdb=" N GLY B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 54 Processing helix chain 'A' and resid 170 through 180 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 249 through 261 removed outlier: 3.592A pdb=" N GLU A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 336 through 339 No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.523A pdb=" N TYR A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.912A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 472 through 495 removed outlier: 3.541A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 54 Processing helix chain 'D' and resid 170 through 180 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 226 through 242 Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.592A pdb=" N GLU D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 296 through 304 Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'D' and resid 336 through 339 No H-bonds generated for 'chain 'D' and resid 336 through 339' Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 360 through 373 removed outlier: 3.523A pdb=" N TYR D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 396 through 403 removed outlier: 3.912A pdb=" N LEU D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 437 through 450 Processing helix chain 'D' and resid 472 through 495 removed outlier: 3.541A pdb=" N GLY D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 54 Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 226 through 242 Processing helix chain 'F' and resid 249 through 261 removed outlier: 3.593A pdb=" N GLU F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 296 through 304 Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 328 through 334 Processing helix chain 'F' and resid 336 through 339 No H-bonds generated for 'chain 'F' and resid 336 through 339' Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 360 through 373 removed outlier: 3.524A pdb=" N TYR F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 394 Processing helix chain 'F' and resid 396 through 403 removed outlier: 3.912A pdb=" N LEU F 403 " --> pdb=" O LEU F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 419 Processing helix chain 'F' and resid 437 through 450 Processing helix chain 'F' and resid 472 through 495 removed outlier: 3.541A pdb=" N GLY F 481 " --> pdb=" O ARG F 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 54 Processing sheet with id= A, first strand: chain 'B' and resid 286 through 289 Processing sheet with id= B, first strand: chain 'B' and resid 378 through 381 Processing sheet with id= C, first strand: chain 'B' and resid 408 through 411 Processing sheet with id= D, first strand: chain 'B' and resid 456 through 460 Processing sheet with id= E, first strand: chain 'A' and resid 286 through 289 Processing sheet with id= F, first strand: chain 'A' and resid 378 through 381 Processing sheet with id= G, first strand: chain 'A' and resid 408 through 411 Processing sheet with id= H, first strand: chain 'A' and resid 456 through 460 Processing sheet with id= I, first strand: chain 'D' and resid 286 through 289 Processing sheet with id= J, first strand: chain 'D' and resid 378 through 381 Processing sheet with id= K, first strand: chain 'D' and resid 408 through 411 Processing sheet with id= L, first strand: chain 'D' and resid 456 through 460 Processing sheet with id= M, first strand: chain 'F' and resid 286 through 289 Processing sheet with id= N, first strand: chain 'F' and resid 378 through 381 Processing sheet with id= O, first strand: chain 'F' and resid 408 through 411 Processing sheet with id= P, first strand: chain 'F' and resid 456 through 460 540 hydrogen bonds defined for protein. 1584 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: 3.12 Time building geometry restraints manager: 5.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 524 1.03 - 1.23: 0 1.23 - 1.42: 5068 1.42 - 1.62: 6480 1.62 - 1.81: 44 Bond restraints: 12116 Sorted by residual: bond pdb=" C3 LDP D 501 " pdb=" O1 LDP D 501 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C3 LDP B 501 " pdb=" O1 LDP B 501 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C3 LDP A 501 " pdb=" O1 LDP A 501 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C3 LDP F 501 " pdb=" O1 LDP F 501 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" C4 LDP A 501 " pdb=" O2 LDP A 501 " ideal model delta sigma weight residual 1.355 1.402 -0.047 2.00e-02 2.50e+03 5.43e+00 ... (remaining 12111 not shown) Histogram of bond angle deviations from ideal: 79.27 - 90.21: 32 90.21 - 101.15: 5 101.15 - 112.09: 6751 112.09 - 123.03: 9450 123.03 - 133.97: 666 Bond angle restraints: 16904 Sorted by residual: angle pdb=" CA ALA C 52 " pdb=" CB ALA C 52 " pdb=" HB3 ALA C 52 " ideal model delta sigma weight residual 109.00 79.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" CA ALA H 52 " pdb=" CB ALA H 52 " pdb=" HB3 ALA H 52 " ideal model delta sigma weight residual 109.00 79.31 29.69 3.00e+00 1.11e-01 9.79e+01 angle pdb=" CA ALA G 52 " pdb=" CB ALA G 52 " pdb=" HB3 ALA G 52 " ideal model delta sigma weight residual 109.00 79.33 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" CA ALA E 52 " pdb=" CB ALA E 52 " pdb=" HB3 ALA E 52 " ideal model delta sigma weight residual 109.00 79.37 29.63 3.00e+00 1.11e-01 9.75e+01 angle pdb=" CA ALA G 52 " pdb=" CB ALA G 52 " pdb=" HB1 ALA G 52 " ideal model delta sigma weight residual 109.00 79.60 29.40 3.00e+00 1.11e-01 9.60e+01 ... (remaining 16899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 6668 13.80 - 27.61: 272 27.61 - 41.41: 52 41.41 - 55.22: 16 55.22 - 69.02: 8 Dihedral angle restraints: 7016 sinusoidal: 2864 harmonic: 4152 Sorted by residual: dihedral pdb=" CA ILE G 42 " pdb=" CB ILE G 42 " pdb=" CG1 ILE G 42 " pdb=" CD1 ILE G 42 " ideal model delta sinusoidal sigma weight residual 60.00 113.79 -53.79 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ILE C 42 " pdb=" CB ILE C 42 " pdb=" CG1 ILE C 42 " pdb=" CD1 ILE C 42 " ideal model delta sinusoidal sigma weight residual 60.00 113.75 -53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ILE H 42 " pdb=" CB ILE H 42 " pdb=" CG1 ILE H 42 " pdb=" CD1 ILE H 42 " ideal model delta sinusoidal sigma weight residual 60.00 113.75 -53.75 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 7013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 1096 0.022 - 0.045: 341 0.045 - 0.067: 143 0.067 - 0.089: 52 0.089 - 0.112: 52 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA ILE B 409 " pdb=" N ILE B 409 " pdb=" C ILE B 409 " pdb=" CB ILE B 409 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 chirality pdb=" CA ILE D 409 " pdb=" N ILE D 409 " pdb=" C ILE D 409 " pdb=" CB ILE D 409 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.11e-01 chirality pdb=" CA ILE A 466 " pdb=" N ILE A 466 " pdb=" C ILE A 466 " pdb=" CB ILE A 466 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 1681 not shown) Planarity restraints: 2136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 166 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.56e-01 pdb=" N PRO F 167 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 166 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.46e-01 pdb=" N PRO B 167 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 166 " 0.015 5.00e-02 4.00e+02 2.29e-02 8.42e-01 pdb=" N PRO A 167 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.013 5.00e-02 4.00e+02 ... (remaining 2133 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 196 2.25 - 2.84: 6184 2.84 - 3.43: 17860 3.43 - 4.01: 24751 4.01 - 4.60: 35799 Nonbonded interactions: 84790 Sorted by model distance: nonbonded pdb="HG13 ILE E 42 " pdb="HD12 ILE E 42 " model vdw 1.666 1.952 nonbonded pdb="HG13 ILE H 42 " pdb="HD12 ILE H 42 " model vdw 1.667 1.952 nonbonded pdb="HG13 ILE C 42 " pdb="HD12 ILE C 42 " model vdw 1.667 1.952 nonbonded pdb="HG13 ILE G 42 " pdb="HD12 ILE G 42 " model vdw 1.668 1.952 nonbonded pdb="HG12 ILE E 42 " pdb="HD11 ILE E 42 " model vdw 1.676 1.952 ... (remaining 84785 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' selection = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 S 36 5.16 5 C 7192 2.51 5 N 1932 2.21 5 O 2156 1.98 5 H 524 0.53 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=0.00 max=1.00 mean=0.95 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: 0.470 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: 0.450 Extract box with map and model: 1.980 Check model and map are aligned: 0.170 Process input model: 33.020 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.002 0.048 11592 Z= 0.128 Angle : 0.406 3.557 15712 Z= 0.230 Chirality : 0.032 0.112 1684 Planarity : 0.002 0.023 2068 Dihedral : 8.305 69.020 4252 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 45.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.67 % 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: 2.23 (0.24), residues: 1396 helix: 2.56 (0.20), residues: 760 sheet: -0.61 (0.47), residues: 136 loop : 0.49 (0.28), residues: 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.318 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1783 time to fit residues: 22.5381 Evaluate side-chains 77 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3995 Evaluate side-chains 7 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 6 time to evaluate : 0.020 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 0.7321 time to fit residues: 4.4418 Evaluate side-chains 3 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 0.0170 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 0.0170 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11592 Z= 0.173 Angle : 0.470 5.250 15712 Z= 0.250 Chirality : 0.037 0.183 1684 Planarity : 0.005 0.068 2068 Dihedral : 4.197 52.100 1568 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 58.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.67 % 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: 1.12 (0.22), residues: 1396 helix: 1.21 (0.18), residues: 788 sheet: -0.69 (0.46), residues: 136 loop : 0.64 (0.28), residues: 472 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.1786 time to fit residues: 17.8514 Evaluate side-chains 75 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4257 Evaluate side-chains 3 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.024 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.9282 time to fit residues: 2.8281 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 0.1980 chunk 110 optimal weight: 20.0000 chunk 122 optimal weight: 0.0980 chunk 42 optimal weight: 0.0170 chunk 99 optimal weight: 2.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11592 Z= 0.181 Angle : 0.576 9.354 15712 Z= 0.288 Chirality : 0.036 0.134 1684 Planarity : 0.004 0.049 2068 Dihedral : 4.276 45.525 1568 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 60.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.33 % 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: 0.86 (0.22), residues: 1396 helix: 1.02 (0.19), residues: 764 sheet: -0.71 (0.46), residues: 136 loop : 0.48 (0.28), residues: 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.329 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: 1 outliers final: 1 residues processed: 87 average time/residue: 0.1789 time to fit residues: 18.1951 Evaluate side-chains 69 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2877 time to fit residues: 0.7579 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2757 time to fit residues: 2.5920 Evaluate side-chains 1 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.0470 chunk 117 optimal weight: 0.0570 chunk 35 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 11592 Z= 0.157 Angle : 0.463 6.127 15712 Z= 0.239 Chirality : 0.036 0.163 1684 Planarity : 0.003 0.025 2068 Dihedral : 4.235 40.367 1568 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 61.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1396 helix: 0.62 (0.18), residues: 784 sheet: -0.74 (0.46), residues: 136 loop : 0.35 (0.27), residues: 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.285 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: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1846 time to fit residues: 16.5559 Evaluate side-chains 68 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4410 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.3506 time to fit residues: 2.7396 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 0.1980 chunk 112 optimal weight: 0.0970 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 0.0980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 11592 Z= 0.119 Angle : 0.436 6.243 15712 Z= 0.224 Chirality : 0.037 0.235 1684 Planarity : 0.003 0.025 2068 Dihedral : 3.882 34.395 1568 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 57.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1396 helix: 1.00 (0.18), residues: 788 sheet: -0.72 (0.46), residues: 136 loop : 0.29 (0.27), residues: 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.296 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: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1714 time to fit residues: 15.7487 Evaluate side-chains 65 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4241 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.3107 time to fit residues: 2.6614 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 20.0000 chunk 25 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 0.0010 chunk 131 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 overall best weight: 1.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 11592 Z= 0.133 Angle : 0.436 5.019 15712 Z= 0.230 Chirality : 0.035 0.180 1684 Planarity : 0.003 0.041 2068 Dihedral : 3.797 30.148 1568 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 65.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1396 helix: 1.02 (0.18), residues: 788 sheet: -0.77 (0.45), residues: 136 loop : 0.15 (0.27), residues: 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.370 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: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1801 time to fit residues: 16.8020 Evaluate side-chains 68 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4826 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.3080 time to fit residues: 2.6556 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 110 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 0.0020 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.1750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11592 Z= 0.137 Angle : 0.426 3.964 15712 Z= 0.221 Chirality : 0.034 0.126 1684 Planarity : 0.003 0.025 2068 Dihedral : 3.796 29.093 1568 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 64.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1396 helix: 1.22 (0.19), residues: 784 sheet: -0.76 (0.45), residues: 136 loop : 0.19 (0.26), residues: 476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1695 time to fit residues: 15.2276 Evaluate side-chains 66 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4030 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.024 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2731 time to fit residues: 2.5846 Evaluate side-chains 2 residues out of total 11 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.0070 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 0.0050 chunk 89 optimal weight: 0.0970 chunk 64 optimal weight: 0.0030 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: